Random forest classifier improving phenylketonuria screening performance in two Chinese populations

Phenylketonuria (PKU) is a genetic disorder with amino acid metabolic defect, which does great harms to the development of newborns and children. Early diagnosis and treatment can effectively prevent the disease progression. Here we developed a PKU screening model using random forest classifier (RFC) to improve PKU screening performance with excellent sensitivity, false positive rate (FPR) and positive predictive value (PPV) in all the validation dataset and two testing Chinese populations. RFC represented outstanding advantages comparing several different classification models based on machine learning and the traditional logistic regression model. RFC is promising to be applied to neonatal PKU screening.

H-NS Represses Biofilm Formation and c-di-GMP Synthesis in Vibrio parahaemolyticus

OBJECTIVE

This study aimed to investigate the regulation of histone-like nucleoid structuring protein (H-NS) on biofilm formation and cyclic diguanylate (c-di-GMP) synthesis in Vibrio parahaemolyticus RIMD2210633.

METHODS

Regulatory mechanisms were analyzed by the combined utilization of crystal violet staining, quantification of c-di-GMP, quantitative real-time polymerase chain reaction, LacZ fusion, and electrophoretic-mobility shift assay.

RESULTS

The deletion of hns enhanced the biofilm formation and intracellular c-di-GMP levels in V. parahaemolyticus RIMD2210633. H-NS can bind the upstream promoter-proximal DNA regions of scrA, scrG, VP0117, VPA0198, VPA1176, VP0699, and VP2979 to repress their transcription. These genes encode a group of proteins with GGDEF and/or EAL domains associated with c-di-GMP metabolism.

CONCLUSION

One of the mechanisms by which H-NS represses the biofilm formation by V. parahaemolyticus RIMD2210633 may be via repression of the production of intracellular c-di-GMP.

Simultaneous and efficient removal of multiple heavy metal(loid)s from aqueous solutions using Fe/Mn (hydr)oxide and phosphate mineral composites synthesized by regulating the proportion of Fe(II), Fe(III), Mn(II) and PO43

In this work, a novel adsorbent FMPs consisting of Fe/Mn (hydr)oxides and phosphate minerals was synthesized by regulating the proportion of Fe(II), Fe(III), Mn(II) and PO₄^3-, and its removal behaviors and possible mechanisms for Cd(II), Pb(II), Cu(II), Zn(II), As(III), Sb(III), As(V) and Sb(V) were systematically investigated. Batch adsorption experiments revealed that the adsorption process of FMPs to these metal(loid) ions conformed to pseudo-second-order (R² > 0.99) and Redlich-Peterson (R² > 0.94) models in the mono-component system, demonstrating a hybrid chemical reaction-adsorption process. In addition, the solution pH and ionic strength could affect the adsorption capacity of FMPs to heavy metal(loid)s with varying degrees. Besides, FMPs presented feasible stability and reusability even after four cycles. Combining the macroscopic and microscopic characteristics, the adsorption mechanisms of FMPs mainly included surface complexation, electrostatic adsorption, inner-sphere complexation, hydrogen bonding, redox and pore-filling. In a multi-component system, FMPs exhibited an excellent affinity for capturing Pb(II) and Sb(III/V). This work provides an alternative method for designing and developing a series of novel adsorbent in removing multiple heavy metal(loid)s from wastewater, and demonstrated its application prospect in the remediation of multi-metal(loid) composite polluted water.

IFITM3 restricts virus-induced inflammatory cytokine production by limiting Nogo-B mediated TLR responses

Interferon-induced transmembrane protein 3 (IFITM3) is a restriction factor that limits viral pathogenesis and exerts poorly understood immunoregulatory functions. Here, using human and mouse models, we demonstrate that IFITM3 promotes MyD88-dependent, TLR-mediated IL-6 production following exposure to cytomegalovirus (CMV). IFITM3 also restricts IL-6 production in response to influenza and SARS-CoV-2. In dendritic cells, IFITM3 binds to the reticulon 4 isoform Nogo-B and promotes its proteasomal degradation. We reveal that Nogo-B mediates TLR-dependent pro-inflammatory cytokine production and promotes viral pathogenesis in vivo, and in the case of TLR2 responses, this process involves alteration of TLR2 cellular localization. Nogo-B deletion abrogates inflammatory cytokine responses and associated disease in virus-infected IFITM3-deficient mice. Thus, we uncover Nogo-B as a driver of viral pathogenesis and highlight an immunoregulatory pathway in which IFITM3 fine-tunes the responsiveness of myeloid cells to viral stimulation.

Relationship between vitamin D receptor gene polymorphisms and second acid-fast bacilli smear-positive during treatment for tuberculosis patients

PURPOSE

Tuberculosis (TB) treatment is associated with Vitamin D. This study aimed to explore the relationship between Vitamin D receptor (VDR) gene polymorphisms and second acid-fast bacilli (AFB) smear-positive during treatment for TB patients.

METHODS

This was a cross-sectional study. Seven hundred and thirty-one TB patients whose single nucleotide polymorphism site (SNPs) of VDR gene were detected from December 2019 to December 2020 in XinJiang of China. The genotypic distributions in each group were tested separately for Hardy-Weinberg equilibrium. The tetragram test was used to construct haplotypes to evaluate the association between each haplotype and second AFB smear-positive occurrence.

RESULTS

No significant deviations were observed with all the four polymorphism sites in the genotypic distributions (P>0.05). Linkage disequilibrium (LD) analysis showed that there was LD between SNPs of VDR gene (r²=0.74, D`>0.9). Each haplotype was not considered to be the influencing factor of second AFB smear-positive.

CONCLUSIONS

There is no association between VDR gene polymorphism (ApaI, BsmI, FokI and TaqI) and second AFB smear-positive.

A blaSIM-1 and mcr-9.2 harboring Klebsiella michiganensis strain reported and genomic characteristics of Klebsiella michiganensis

As a newly emerging Klebsiella pathogen, more and more Klebsiella michiganensis drug resistant strains have been reported in recent years, which posed serious threats to public health. Here we first reported a multidrug-resistant K. michiganensis strain 12084 with two blaSIM-1 and one mcr-9.2 genes isolated from the sputum specimen of a patient in the Second Affiliated Hospital of Zhejiang University School of Medicine and analyzed its genetic basis and drug-resistance phenotypes. Genetic analysis showed that this strain harbored three different incompatibility groups (IncHI2, IncHI5, and IncFIIpKPHS2:IncFIB-4.1) of plasmids (p12084-HI2, p12084-HI5, and p12084-FII). A total of 26 drug-resistance genes belonging to 12 classes of antibiotics were identified, most of which (24) were located on two plasmids (p12084-HI2 and p12084-HI5). Interestingly, two blaSIM-1 genes were identified to locate on p12084-HI2 and p12084-HI5, respectively, both of which were embedded in In630, indicating their genetic homogeny. It was noting that one blaSIM-1 gene was situated in a novel unit transposon (referred to as Tn6733) on the p12084-HI5 plasmid. We also discovered an mcr-9.2 gene on the p12084-HI2 plasmid. To the best of our knowledge, this is the first report of a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain. We then investigated the population structure/classification, and antibiotic resistance for all 275 availably global K. michiganensis genomes. Population structure revealed that K. michiganensis could be divided into two main clades (Clade 1 and Clade 2); the most popular ST29 was located in Clade 1, while other common STs (such as ST50, ST27, and ST43) were located in Clade 2. Drug-resistance analysis showed 25.5% of the K. michiganensis strains (70/275) harboring at least one carbapenemase gene, indicating severe drug resistance of K. michiganensis beyond our imagination; this is a dangerous trend and should be closely monitored, especially for ST27 K. michiganensis with the most drug-resistant genes among all the STs. Overall, we reported a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain, and further revealed the population structure/classification, and drug-resistance of K. michiganensis, which provided an important framework, reference, and improved understanding of K. michiganensis.

Removal of heavy metal(loid)s from aqueous solution by biogenic FeS-kaolin composite: Behaviors and mechanisms

In this work, a green adsorbent, biogenic FeS-kaolin composite (KL-FeS) was synthesized by sulfate-reducing bacteria (SRB) mediation, and its potential for Cd(II), Pb(II), Cu(II), Zn(II), As(III) and Sb(III) removal was evaluated. Among prepared composites, the KL-FeS synthesized at a concentration of 2 g/L kaolin performed a better removal efficiency on heavy metal(loid)s and the adsorption results followed the pseudo-second-order and Redlich-Peterson models, indicating that the adsorption was a hybrid chemical reaction-adsorption process. Additionally, the maximum adsorption capacities of Cd(II), Pb(II), Cu(II), Zn(II), As(III) and Sb(III) on KL-FeS in monocomponent system were 71.71, 133.54, 51.90, 54.41, 38.71 and 96.38 mg/g, respectively (pH = 5.0 ± 0.1, T = 25 °C). In addition, the increase of pH and ionic strength promoted the adsorption capacities of KL-FeS for metal-(loid)s. Moreover, FTIR, XPS and XRD analyses supported that surface complexation, hydrogen bonding, ion exchange, electrostatic interaction and chemical precipitation were predominately mechanisms involved in the adsorption process. Furthermore, KL-FeS displayed higher affinity for Pb(II), Sb(III) and Cu(II) in the multi-component system. This work highlighted the potential of biogenic FeS-kaolin composite for simultaneous removal of multiple heavy metal(loid)s under aerobic conditions.

Hypertriton Production in p-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The study of nuclei and antinuclei production has proven to be a powerful tool to investigate the formation mechanism of loosely bound states in high-energy hadronic collisions. The first measurement of the production of _{Λ}^{3}H in p-Pb collisions at sqrt[s_{NN}]=5.02  TeV is presented in this Letter. Its production yield measured in the rapidity interval -1<y<0 for the 40% highest-multiplicity p-Pb collisions is dN/dy=[6.3±1.8(stat)±1.2(syst)]×10^{-7}. The measurement is compared with the expectations of statistical hadronization and coalescence models, which describe the nucleosynthesis in hadronic collisions. These two models predict very different yields of the hypertriton in charged particle multiplicity environments relevant to small collision systems such as p-Pb, and therefore the measurement of dN/dy is crucial to distinguish between them. The precision of this measurement leads to the exclusion with a significance larger than 6.9σ of some configurations of the statistical hadronization model, thus constraining the theory behind the production of loosely bound states at hadron colliders.

Innate immune responses against the fungal pathogen Candida auris

Candida auris is a multidrug-resistant human fungal pathogen responsible for nosocomial outbreaks worldwide. Although considerable progress has increased our understanding of the biological and clinical aspects of C. auris, its interaction with the host immune system is only now beginning to be investigated in-depth. Here, we compare the innate immune responses induced by C. auris BJCA001 and Candida albicans SC5314 in vitro and in vivo. Our results indicate that C. auris BJCA001 appears to be less immunoinflammatory than C. albicans SC5314, and this differential response correlates with structural features of the cell wall.

Candida auris is a multidrug-resistant human fungal pathogen responsible for nosocomial outbreaks worldwide. Here, the authors identify differential innate immune responses induced by C. auris and Candida albicans in vitro and in vivo, which correlate with structural features of the cell wall.

Unraveling the Phase Transition and Luminescence Tuning of Pb-Free Cs-Cu-I Perovskites Enabled by Reaction Temperature and Polar Solvent

Ternary Pb-free Cs-Cu-I perovskites have attracted widespread attention because of their excellent optical properties and environmentally friendly advantages. Herein, two different Pb-free ternary Cs₃Cu₂I₅ nanocrystals (NCs) and CsCu₂I₃ microrods (MRs) were synthesized via a heating method. The phase and morphology transition from blue emission of Cs₃Cu₂I₅ NCs to yellow emission of CsCu₂I₃ MRs could be tuned effectively by manipulating the reaction temperature, decreasing the maximum photoluminescence quantum yields (PLQYs) from 82.7% to ∼10%. More interestingly, the Cs₃Cu₂I₅ NCs could self-assemble into stacking chains, which exhibited a strong dependence on the polarity of solvents. In addition, it was demonstrated that the rapid phase transition and luminescence tuning between Cs₃Cu₂I₅ and CsCu₂I₃ films took only a few seconds by direct heating or exposure to the polar solvent. This work may deepen the understanding of the phase transition process in Cu-based perovskites and provide a fluorescence material with a short switching time for anticounterfeiting applications.

Electroluminescent white light-emitting diodes with cadimum-free Cu-In-Zn-S nanocrystals sandwiched between two TFB layers

A high color rendering index (CRI) and stable spectra under different voltages are important parameters for large-area planar light sources. However, the spectrum of most electroluminescent white light-emitting diodes (el-WLEDs) with a single emissive layer (EML) varies with a changing voltage. Herein, an el-WLED is fabricated based on Cd-free Cu-In-Zn-S (CIZS)/ZnS nanocrystals (NCs) and poly [(9,9-dioctylfluorenyl-2,7-diyl)-co-(4,4'-(N-(p-butylphenyl))diphenylamine)] (TFB) as double EMLs, which exhibit white-light emission with a high CRI value of 91 and commission internationale de l'éclairage (CIE) color coordinates of (0.33, 0.33). Meanwhile, it has a stable spectrum under voltage up to 7 V and a maximum luminance up to 679 cd/m² with a low turn-on voltage of 2.2 V. This work provides a foundation for Cd-free el-WLEDs with high CRI and stable spectra.

Ultrasmall Fe-doped carbon dots nanozymes for photoenhanced antibacterial therapy and wound healing

Pathogenic bacteria pose a devastating threat to public health. However, because of the growing bacterial antibiotic resistance, there is an urgent need to develop alternative antibacterial strategies to the established antibiotics. Herein, iron-doped carbon dots (Fe-CDs, ∼3 nm) nanozymes with excellent photothermal conversion and photoenhanced enzyme-like properties are developed through a facile one-pot pyrolysis approach for synergistic efficient antibacterial therapy and wound healing. In particular, Fe doping endows CDs with photoenhanced peroxidase (POD)-like activity, which lead to the generation of heat and reactive oxygen species (ROS) for Gram-positive and Gram-negative bacteria killing. This study demonstrates Fe-CDs have significant wound healing efficiency of Fe-CDs by preventing infection, promoting fibroblast proliferation, angiogenesis, and collagen deposition. Furthermore, the ultrasmall size of Fe-CDs possesses good biocompatibility favoring clinical translation. We believe that the nanozyme-mediated therapeutic platform presented here is expected to show promising applications in antibacterial.

•

Iron doped carbon dots (Fe-CDs, ~3 nm) exhibited excellent photothermal conversion and photoenhanced enzyme-like properties.

•

Fe-CDs as nanozyme and photothermal agent possess outstanding antibacterial ratio against both S. aureus and E. coli.

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The photoresponsive nanozyme-mediated therapeutic platform exhibited great promise for bacterial-infected wound healing.

POS0664 RADIOGRAPHIC CHANGE IN PATIENTS WITH RHEUMATOID ARTHRITIS AND ESTIMATED BASELINE YEARLY PROGRESSION ≥5 OR <5: POST HOC ANALYSIS OF TWO PHASE 3 TRIALS OF FILGOTINIB

Background

In some patients (pts) with rheumatoid arthritis (RA), especially those with joint damage early in the disease, first-line methotrexate (MTX) treatment may not suffice to prevent further rapid radiographic progression (RRP).1 In FINCH 1 (NCT02889796), filgotinib 200 mg (FIL200) and 100 mg (FIL100) reduced change in modified total Sharp score (mTSS) vs placebo (PBO) in pts with RA and inadequate response to MTX (MTX-IR).2 In FINCH 3 (NCT02886728), FIL200 and FIL100 reduced change in mTSS vs MTX monotherapy (MTX mono) in MTX-naïve pts.3

Objectives

To evaluate, via post hoc analysis of 2 trials, filgotinib’s effects on radiographic progression vs MTX mono in pts with estimated baseline (BL) yearly progression ≥5 or <5 mTSS units/year.

Methods

The double-blind 52-week (W) FINCH 1 study randomised MTX-IR pts with moderate–severe active RA to FIL200 or FIL100, subcutaneous adalimumab (ADA) 40 mg, or PBO; at W24, PBO pts were rerandomised blinded to FIL200 or FIL100; all took stable background MTX.2 In FINCH 3, MTX-naïve pts were randomised, blinded, to FIL200 + MTX, FIL100 + MTX, FIL200 alone, or MTX mono for up to W52.3 This analysis examined subgroups by estimated BL yearly progression (BL mTSS/duration in years of RA diagnosis), based on ≥5 or <5 mTSS units/year,4 a threshold commonly used to define RRP. We assessed effects of filgotinib vs ADA or PBO in mTSS change from BL (CFB) at W24/W52 (using a mixed model for repeated measures) and percentages with no W24 progression (mTSS change ≤0, ≤0.5, ≤smallest detectable change [SDC], using Fisher’s exact test).

Results

At BL, 558/1755 MTX-IR and 787/1249 MTX-naïve pts had BL estimated yearly progression ≥5. Median mTSS in pts with BL yearly progression ≥5 and <5 was 53.25 vs 5.00 respectively in the MTX-IR trial and 6.00 vs 2.50 in the MTX-naïve trial. At W24, the mTSS CFB in pts with BL yearly progression ≥5 and <5 was 0.84 and 0.22 in MTX-IR pts taking PBO + MTX, and 0.67 and 0.25 in MTX-naïve pts taking MTX mono. At W52, in pts with BL yearly progression ≥5, FIL200 + MTX reduced mTSS change vs PBO + MTX in the MTX-IR trial and vs MTX mono in the MTX-naïve trial (Figure 1). At W24, among pts with estimated BL yearly progression ≥5, FIL200 + MTX increased odds of no progression (≤0.5 or ≤0) vs PBO + MTX in MTX-IR pts and vs MTX mono in MTX-naïve pts (Table 1).

Table 1.

Ratio of no radiographic progression at W24

FINCH 1: MTX-IRFIL200 + MTXFIL100 + MTXADA + MTXPBO + MTXBL yearly progression≥5(n = 138)<5(n = 267)≥5(n = 139)<5(n = 265)≥5(n = 91)<5(n = 180)≥5(n = 101)<5(n = 250)% with no progression (≤0.5)87.797.088.592.587.993.976.291.6OR2.22*2.97*2.40*1.12††††% with no progression (≤0)80.491.881.388.380.289.467.386.4OR2.00*1.752.11*1.19††††% with no progression (≤SDC [1.36])91.398.192.196.692.395.681.294.0OR2.43*3.35*2.70*1.82††††FINCH 3: MTX-naïveFIL200 + MTXFIL100 + MTXFIL200 monoMTXBL yearly progression≥5<5≥5<5≥5<5≥5<5(n = 221)(n = 134)(n = 121)(n = 63)(n = 115)(n = 58)(n = 224)(n = 132)% with no progression (≤0.5)86.994.083.593.789.689.778.687.9OR1.81*2.171.382.032.34*1.20††% with no progression (≤0)78.783.672.784.180.087.967.980.3OR1.75*1.251.261.31.89*1.79††% with no progression (≤SDC [1.53])93.797.891.796.895.796.689.395.5OR1.772.081.331.452.641.33††

MTX-IR ORs are FIL vs PBO + MTX; MTX-naïve are FIL vs MTX. *Nominal P<.05. †Not applicable.

ADA, adalimumab; FIL, filgotinib; IR, inadequate response; mTSS, modified total Sharp score; MTX, methotrexate; OR, odds ratio; SDC, smallest detectable change; W, week.

Conclusion

These data suggest filgotinib’s inhibition of radiographic progression was numerically greater than MTX monotherapy in RA pts with high estimated BL yearly progression. In those with a more moderate estimated rate of progression, filgotinib suppressed progression comparably to ADA and/or MTX.

References

[1]Smolen J et al. Ann Rheum Dis 2018;77:1566–1572.

[2]Combe B et al. Ann Rheum Dis 2021;80:848–858.

[3]Westhovens R et al. Ann Rheum Dis 2021;80:727–738.

[4]Vastesaeger N et al. Rheumatology. 2009;48:1114–1121.

Acknowledgements

This study was funded by Gilead Sciences, Inc., Foster City, CA. Medical writing support was provided by Rob Coover, MPH, of AlphaScientia, LLC, San Francisco, CA; and funded by Gilead Sciences, Inc., Foster City, CA. Funding for this analysis was provided by Gilead Sciences, Inc. The sponsors participated in the planning, execution, and interpretation of the research.

Disclosure of Interests

Yoshiya Tanaka Speakers bureau: AbbVie, Amgen, Astellas, AstraZeneca, Behringer-Ingelheim, Bristol-Myers Squibb, Chugai, Eisai, Eli Lilly, Gilead, Mitsubishi-Tanabe, and YL Biologics, Grant/research support from: AbbVie, Asahi-Kasei, Boehringer-Ingelheim, Chugai, Corrona, Daiichi Sankyo, Eisai, Kowa, Mitsubishi-Tanabe, and Takeda, Tatsuya Atsumi Paid instructor for: Gilead Sciences, Inc.; Mitsubishi Tanabe; Chugai; Astellas Pharma; Takeda; Pfizer; AbbVie: Eisai; Daiichi Sankyo; Bristol-Myers Squibb; UCB Japan Co. Ltd.; Eli Lilly Japan K.K., Otsuka Pharmaceutical Co., Ltd.; and Alexion Inc., Grant/research support from: Gilead Sciences, Inc.; Mitsubishi Tanabe; Chugai; Astellas Pharma; Takeda; Pfizer; AbbVie: Eisai; Daiichi Sankyo; Bristol-Myers Squibb; UCB Japan Co. Ltd.; Eli Lilly Japan K.K., Otsuka Pharmaceutical Co., Ltd.; and Alexion Inc., Daniel Aletaha Speakers bureau: AbbVie; Amgen; Celgene; Eli Lilly; Medac; Merck; Novartis; Pfizer; Roche; Sandoz; and Sanofi/Genzyme; Bristol-Myers Squibb, Merck Sharp & Dohme, and UCB, Consultant of: Janssen; AbbVie; Amgen; Celgene; Eli Lilly; Medac; Merck; Novartis; Pfizer; Roche; Sandoz; and Sanofi/Genzyme, Grant/research support from: AbbVie, Merck Sharp & Dohme, Novartis, and Roche, Robert B.M. Landewé Paid instructor for: AbbVie, AstraZeneca, Bristol-Myers Squibb, Eli Lilly, Galapagos NV, Novartis, Pfizer, and UCB, Consultant of: AbbVie, AstraZeneca, Bristol-Myers Squibb, Eli Lilly, Galapagos NV, Novartis, Pfizer, and UCB, Beatrix Bartok Shareholder of: Gilead Sciences, Inc., Employee of: Gilead Sciences, Inc, Alena Pechonkina Shareholder of: Gilead Sciences, Inc., Employee of: Gilead Sciences, Inc., Zhaoyu Yin Shareholder of: Gilead Sciences, Inc., Employee of: Gilead Sciences, Inc., Ling Han Shareholder of: Gilead Sciences, Inc., Employee of: Gilead Sciences, Inc., Kahaku Emoto Shareholder of: Gilead Sciences, Inc., Employee of: Gilead Sciences K.K., Shungo Kano Shareholder of: Gilead Sciences, Inc., Employee of: Gilead Sciences K.K., Vijay Rajendran Employee of: Galapagos BV, Tsutomu Takeuchi Speakers bureau: AbbVie, Ayumi Pharmaceutical Corporation, Bristol-Myers Squibb, Chugai, Daiichi Sankyo, Dainippon Sumitomo Eisai, Eli Lilly Japan, Mitsubishi-Tanabe, Novartis, Pfizer Japan, Sanofi, and Gilead Sciences, Inc., Consultant of: Astellas, Chugai, and Eli Lilly Japan, Grant/research support from: AbbVie, Asahi Kasei, Astellas, Chugai, Daiichi Sankyo, Eisai, Mitsubishi-Tanabe, Shionogi, Takeda, and UCB Japan

Comparisons of prognosis prediction accuracy between modified and unmodified versions of 8th edition ypTNM

Background

The prognostic value of the existing 8^th edition post-neoadjuvant treatment (ypTNM) appears to be limited, and necessary reassessment and modification should be carried out as needed. This study aimed to compare the prognosis prediction accuracy of modified and unmodified versions of the 8^th edition ypTNM.

Methods

Esophageal cancer patients who had received neoadjuvant therapy from the Surveillance, Epidemiology, and End Results (SEER) database were included in this observational longitudinal study. The median follow-up time was 26 months. All-cause mortality was the outcome variable. Demographic and clinical variables were collected as covariates. Kaplan-Meier (log-rank test) and Cox proportional hazards models were conducted for developing modified ypTNM staging. The concordance index (C-index) was calculated to analyze the discriminative ability of modified ypTNM staging.

Results

Overall, 3,595 patients met inclusion criteria. The 8^th edition staging was not able to significantly discriminate between patients with ypT1- and ypT2-, ypT3- and ypT4-, ypN2- and ypN3- disease, respectively. Using the modified staging, we found that patients with ypT0–2 [hazard ratio (HR) =1.232; 95% confidence interval (CI): 1.053–1.441] and ypT3–4 (HR =1.257; 95% CI: 1.136–1.390) with grade III + IV had a significant risk of death compared to those with grade I + II. As was the case for the ypN0 (HR =1.295; 95% CI: 1.073–1.562) group with middle and upper tumor locations compared to those with low tumor location. The modified staging possessed better homogeneity in terms of the chi-square likelihood ratio (143.443 vs. 102.044), Akaike information criterion (AIC) (32,683.716 vs. 32,719.115), and Schwarz’s Bayesian criterion (SBC) (32,723.496 vs. 32,741.847), as well as better discriminatory ability (C-index of 0.577 vs. 0.560, P=0.045) compared to the 8^th edition staging.

Conclusions

Although the modified ypTNM staging system we created by incorporating tumor grade and location to the original T and N displayed certain prognosis prediction accuracy compared with the 8^th edition ypTNM staging, a larger sample size and prospective studies are needed to explore.

Bacteroides species differentially modulate depression-like behavior via gut-brain metabolic signaling

Gut microbiome disturbances have been widely implicated in major depressive disorder (MDD), although the identity of causal microbial species and the underlying mechanisms are yet to be fully elucidated. Here we show that Bacteroides species enriched in the gut microbiome from MDD patients differentially impact the susceptibility to depressive behaviors. Transplantation of fecal microbiome from MDD patients into antibiotic-treated mice induced anxiety and despair-like behavior and impaired hippocampal neurogenesis. Colonization of Bacteroides fragilis, Bacteroides uniformis, and, to a lesser extent, Bacteroides caccae, but not Bacteroides ovatus, recapitulated the negative effects of MDD microbiome on behavior and neurogenesis. The varying impacts of Bacteroides species were partially explained by differential alternations of tryptophan pathway metabolites and neurotransmitters along the gut-brain axis. Notably, an intensified depletion of cerebral serotonin concurred with the enhanced susceptibility to depression. Together, these findings identify select Bacteroidetes species that contribute to depression susceptibility in mice by metabolic regulation along the gut-brain axis.

Polarization of Λ and Λ[over ¯] Hyperons along the Beam Direction in Pb-Pb Collisions at sqrt[s]_{NN}=5.02 TeV

The polarization of the Λ and Λ[over ¯] hyperons along the beam (z) direction, P_{z}, has been measured in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV recorded with ALICE at the Large Hadron Collider (LHC). The main contribution to P_{z} comes from elliptic flow-induced vorticity and can be characterized by the second Fourier sine coefficient P_{z,s2}=⟨P_{z}sin(2φ-2Ψ_{2})⟩, where φ is the hyperon azimuthal emission angle and Ψ_{2} is the elliptic flow plane angle. We report the measurement of P_{z,s2} for different collision centralities and in the 30%-50% centrality interval as a function of the hyperon transverse momentum and rapidity. The P_{z,s2} is positive similarly as measured by the STAR Collaboration in Au-Au collisions at sqrt[s_{NN}]=200  GeV, with somewhat smaller amplitude in the semicentral collisions. This is the first experimental evidence of a nonzero hyperon P_{z} in Pb-Pb collisions at the LHC. The comparison of the measured P_{z,s2} with the hydrodynamic model calculations shows sensitivity to the competing contributions from thermal and the recently found shear-induced vorticity, as well as to whether the polarization is acquired at the quark-gluon plasma or the hadronic phase.

Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae

Klebsiella pneumoniae (K. pneumoniae) is an important pathogen that can cause severe hospital- and community-acquired infections. To systematically investigate its methylation features, we determined the whole-genome sequences of 14 K. pneumoniae strains covering varying serotypes, multilocus sequence types, clonal groups, viscosity/virulence, and drug resistance. Their methylomes were further characterized using Pacific Biosciences single-molecule real-time and bisulfite technologies. We identified 15 methylation motifs [13 N6-methyladenine (6mA) and two 5-methylcytosine (5mC) motifs], among which eight were novel. Their corresponding DNA methyltransferases were also validated. Additionally, we analyzed the genomic distribution of GATC and CCWGG methylation motifs shared by all strains, and identified differential distribution patterns of some hemi-/un-methylated GATC motifs, which tend to be located within intergenic regions (IGRs). Specifically, we characterized the in vivo methylation kinetics at single-base resolution on a genome-wide scale by simulating the dynamic processes of replication-mediated passive demethylation and MTase-catalyzed re-methylation. The slow methylation of the GATC motifs in the replication origin (oriC) regions and IGRs implicates the epigenetic regulation of replication initiation and transcription. Our findings illustrate the first comprehensive dynamic methylome map of K. pneumoniae at single-base resolution, and provide a useful reference to better understand epigenetic regulation in this and other bacterial species.

Genetic Characterization of Four Groups of Chromosome-Borne Accessory Genetic Elements Carrying Drug Resistance Genes in Providencia

Purpose

The aim of this study was to gain a deeper genomics and bioinformatics understanding of diversification of accessory genetic elements (AGEs) in Providencia.

Methods

Herein, the complete genome sequences of five Providencia isolates from China were determined, and seven AGEs were identified from the chromosomes. Detailed genetic dissection and sequence comparison were applied to these seven AGEs, together with additional 10 chromosomal ones from GenBank (nine of them came from Providencia).

Results

These 17 AGEs were divided into four groups: Tn6512 and its six derivatives, Tn6872 and its two derivatives, Tn6875 and its one derivative, and Tn7 and its four derivatives. These AGEs display high-level diversification in modular structures that had complex mosaic natures, and particularly different multidrug resistance (MDR) regions were presented in these AGEs. At least 52 drug resistance genes, involved in resistance to 15 different categories of antimicrobials and heavy metal, were found in 15 of these 17 AGEs.

Conclusion

Integration of these AGEs into the Providencia chromosomes would contribute to the accumulation and distribution of drug resistance genes and enhance the ability of Providencia isolates to survive under drug selection pressure.

Mechanically Reinforced Silkworm Silk Fiber by Hot Stretching

Silkworm silk, which is obtained from domesticated Bombyx mori (B. mori), can be produced in a large scale. However, the mechanical properties of silkworm silk are inferior to its counterpart, spider dragline silk. Therefore, researchers are continuously exploring approaches to reinforce silkworm silk. Herein, we report a facile and scalable hot stretching process to reinforce natural silk fibers obtained from silkworm cocoons. Experimental results show that the obtained hot-stretched silk fibers (HSSFs) retain the chemical components of the original silk fibers while being endowed with increased β-sheet nanocrystal content and crystalline orientation, leading to enhanced mechanical properties. Significantly, the average modulus of the HSSFs reaches 21.6 ± 2.8 GPa, which is about twice that of pristine silkworm silk fibers (11.0 ± 1.7 GPa). Besides, the tensile strength of the HSSFs reaches 0.77 ± 0.13 GPa, which is also obviously higher than that of the pristine silk (0.56 ± 0.08 GPa). The results show that the hot stretching treatment is effective and efficient for producing superstiff, strong, and tough silkworm silk fibers. We anticipate this approach may be also effective for reinforcing other natural or artificial polymer fibers or films containing abundant hydrogen bonds.

Genomic epidemiology of carbapenemase-producing Klebsiella pneumoniae in china

The rapid spread of carbapenemase-producing Klebsiella pneumoniae (cpKP) poses serious threats to public health, however, the underlying genetic basis for its dissemination is still unknown. We conducted a comprehensive genomic epidemiology analysis on 420 cpKP isolates collected from 70 hospitals in 24 provinces of China during 2009-2017 by short-/long-read sequencing. The results showed that most cpKP isolates were categorized into clonal group 258 (CG258), in which ST11 was the dominant clone. Phylogenetic analysis revealed three major clades including the top one of Clade 3 for CG258 cpKP isolates. Additionally, carbapenemase gene analysis indicated that bla_KPC was dominant in the cpKP isolates, and most bla_KPC genes were located in five major incompatibility (Inc) groups of bla_KPC-harboring plasmids. Importantly, three advantageous combinations of host-bla_KPC-carrying plasmids (Clade 3.1 + 3.2-IncFII_pHN7A8, Clade 3.1 + 3.2-IncFII_pHN7A8:IncR, and Clade 3.3-IncFII_pHN7A8:Inc_pA1763-KPC) were identified to confer cpKP isolates the advantages in both genotypes (strong correlation/co-evolution) and phenotypes (resistance/growth/competition) to facilitate the nationwide spread of ST11/CG258 cpKP. Intriguingly, Bayesian skyline analysis illustrated that the three advantageous combinations might be directly associated with the strong population expansion during 2007-2008 and subsequent maintenance of the population of ST11/CG258 cpKP after 2008. We then examined drug resistance profiles of these cpKP isolates and proposed combination treatment regimens for CG258/non-CG258 cpKP infections. Thus, the findings of our systematical analysis shed light on the molecular epidemiology and genetic basis for the dissemination of ST11/CG258 cpKP in China, and much emphasis should be given to the close monitoring of advantageous cpKP-plasmid combinations.

Measurement of the Groomed Jet Radius and Momentum Splitting Fraction in pp and Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

This article presents groomed jet substructure measurements in pp and Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV with the ALICE detector. The soft drop grooming algorithm provides access to the hard parton splittings inside a jet by removing soft wide-angle radiation. We report the groomed jet momentum splitting fraction, z_{g}, and the (scaled) groomed jet radius, θ_{g}. Charged-particle jets are reconstructed at midrapidity using the anti-k_{T} algorithm with resolution parameters R=0.2 and R=0.4. In heavy-ion collisions, the large underlying event poses a challenge for the reconstruction of groomed jet observables, since fluctuations in the background can cause groomed parton splittings to be misidentified. By using strong grooming conditions to reduce this background, we report these observables fully corrected for detector effects and background fluctuations for the first time. A narrowing of the θ_{g} distribution in Pb-Pb collisions compared to pp collisions is seen, which provides direct evidence of the modification of the angular structure of jets in the quark-gluon plasma. No significant modification of the z_{g} distribution in Pb-Pb collisions compared to pp collisions is observed. These results are compared with a variety of theoretical models of jet quenching, and provide constraints on jet energy-loss mechanisms and coherence effects in the quark-gluon plasma.

VIM-encoding IncpSTY plasmids and chromosome-borne integrative and mobilizable elements (IMEs) and integrative and conjugative elements (ICEs) in Pseudomonas

BACKGROUND

The carbapenem-resistance genes bla_VIM are widely disseminated in Pseudomonas, and frequently harbored within class 1 integrons that reside within various mobile genetic elements (MGEs). However, there are few reports on detailed genetic dissection of bla_VIM-carrying MGEs in Pseudomonas.

METHODS

This study presented the complete sequences of five bla_VIM-2/-4-carrying MGEs, including two plasmids, two chromosomal integrative and mobilizable elements (IMEs), and one chromosomal integrative and conjugative element (ICE) from five different Pseudomonas isolates.

RESULTS

The two plasmids were assigned to a novel incompatibility (Inc) group Inc_pSTY, which included only seven available plasmids with determined complete sequences and could be further divided into three subgroups Inc_pSTY-1/2/3. A detailed sequence comparison was then applied to a collection of 15 MGEs belonging to four different groups: three representative Inc_pSTY plasmids, two Tn6916-related IMEs, two Tn6918-related IMEs, and eight Tn6417-related ICEs and ten of these 15 MGEs were first time identified. At least 22 genes involving resistance to seven different categories of antibiotics and heavy metals were identified within these 15 MGEs, and most of these resistance genes were located within the accessory modules integrated as exogenous DNA regions into these MGEs. Especially, eleven of these 15 MGEs carried the bla_VIM genes, which were located within 11 different concise class 1 integrons.

CONCLUSION

These bla_VIM-carrying integrons were further integrated into the above plasmids, IMEs/ICEs with intercellular mobility. These MGEs could transfer between Pseudomonas isolates, which resulted in the accumulation and spread of bla_VIM among Pseudomonas and thus was helpful for the bacteria to survival from the stress of antibiotics. Data presented here provided a deeper insight into the genetic diversification and evolution of VIM-encoding MGEs in Pseudomonas.

IncFIB-4.1 and IncFIB-4.2 Single-Replicon Plasmids: Small Backbones with Large Accessory Regions

Purpose

To establish a typing scheme for IncFIB replicon and to dissect genomic features of IncFIB-4.1/4.2 single-replicon plasmids.

Methods

A total of 146 representative fully sequenced IncFIB-replicon-containing plasmids were selected to construct a phylogenetic tree of repB_IncFIB sequences. A collection of nine IncFIB-4.1/4.2 single-replicon plasmids from China were fully sequenced here and compared with the first sequenced IncFIB-4.1/4.2 single-replicon plasmids from GenBank to dissect their genomic diversity.

Results

In this study, a repB sequence-based scheme was proposed for grouping IncFIB replicon into seven primary types and further into 70 subtypes. A collection of nine IncFIB-4.1/4.2 single-replicon plasmids were fully sequenced here and compared with the first sequenced IncFIB-4.1/4.2 single-replicon plasmids from GenBank. These 11 plasmids had small backbones and shared only three key backbone markers repB together with its iterons, parABC, and stbD. Each plasmid contained one large accessory region (LAR) inserted into the backbone, and these 11 LARs had significantly distinct profiles of mobile genetic elements (MGEs) and resistance/metabolism gene loci. Antibiotic resistance regions (ARRs; the antibiotic resistance gene-containing genetic elements) were found in seven of these 11 LARs. Besides resistance genes, ARRs carried unit or composite transposons, integrons, and putative resistance units. IncFIB-4.1/4.2 single-replicon plasmids were important vectors of drug resistance genes. This was the first report of three novel MGEs: In1776, Tn6755, and Tn6857.

Conclusion

Data presented here provided a deeper insight into diversity and evolution of IncFIB replicon and IncFIB-4.1/4.2 single-replicon plasmids.

Perioperative Clinical Results of Transcervical and Transhiatal Esophagectomy versus Thoracoscopic Esophagectomy in Patients with Esophageal Carcinoma: A Prospective, Randomized, Controlled Study

Background

This study assessed the efficacy of transcervical and transhiatal esophagectomy versus thoracoscopic esophagectomy in patients with esophageal carcinoma (EC).

Methods

A total of 80 patients with EC were enrolled in this study, including 40 cases in the observation group that received transcervical combine transhiatal esophagectomy and the rest 40 cases of the group that underwent thoracoscopic esophagectomy. The preoperative, intraoperative, and postoperative data were analyzed between the two surgeries, regarding perioperative bleeding, the total number of dissected mediastinal lymph nodes, operative time, number of lymph nodes in the left para-recurrent laryngeal nerve (para-RLN) or the right para-RLN, time in the intensive care unit (ICU), postoperative pain score, the length of postoperative stay (LOPS), PO₂/fraction of inspired oxygen (PO₂/FiO2), pulmonary infection, and lymphatic metastasis.

Results

The operations were successfully performed in all 80 patients. The results showed that patients who underwent transcervical and transhiatal esophagectomy had shorter operations than those with transthoracic esophagectomy (200 minutes vs 235 minutes, Kruskal–Wallis test [Z] = –3.700, P < 0.001). The number of dissected mediastinal lymph nodes in the left para-RLN in the observation group was higher than in the control group (25.0% vs 2.5%, Z = 2.568, P = 0.010). The postoperative pain score day 1 (0.0% vs 17.5%, Z = –4.292, P < 0.001), postoperative pain score day 3 (12.5% vs 37.5%, Z = –3.363, P < 0.001) and 48-h PO₂/FiO2 (290 minutes vs 255 minutes, Z = 3.747, P < 0.001) were significant between the two groups. The LOPS of patients with EC in the observation group was shorter than the control group (7 vs 8, Z = –2.119, P = 0.034). The number of patients receiving transcervical and transhiatal esophagectomy that developed postoperative pulmonary infections was less than the controls (chi-square [χ²] = 4.114, P = 0.043). Moreover, the transcervical and transhiatal esophagectomy was an independent protect factor for postoperative pulmonary infection (odds ratio [OR] =7.801, P = 0.037).

Conclusion

The transcervical and transhiatal esophagectomy is a good operation for treating patients with EC, which may offer an opportunity to treat cases who cannot have thoracotomy.

A Genomic and Bioinformatics View of the Classification and Evolution of Morganella Species and Their Chromosomal Accessory Genetic Elements Harboring Antimicrobial Resistance Genes

In this study, draft-genome sequencing was conducted for 60 Chinese Morganella isolates, and furthermore, 12 of them were fully sequenced. Then, a total of 166 global sequenced Morganella isolates, including the above 60, were collected to perform average nucleotide identity-based genomic classification and core single nucleotide polymorphism-based phylogenomic analysis. A genome sequence-based species classification scheme for Morganella was established, and accordingly, the two conventional Morganella species were redefined as two complexes and further divided into four and two genospecies, respectively. At least 88 acquired antimicrobial resistance genes (ARGs) were disseminated in these 166 isolates and were prevalent mostly in the isolates from hospital settings. IS26/IS15DI, IS10 and IS1R, and Tn3-, Tn21-, and Tn7-subfamily unit transposons were frequently presented in these 166 isolates. Furthermore, a detailed sequence comparison was applied to 18 Morganella chromosomal accessory genetic elements (AGEs) from the fully sequenced 12 isolates, together with 5 prototype AGEs from GenBank. These 23 AGEs were divided into eight different groups belonging to composite/unit transposons, transposable prophages, integrative and mobilizable elements, and integrative and conjugative elements, and they harbored at least 52 ARGs involved in resistance to 15 categories of antimicrobials. Eleven of these 23 AGEs acquired large accessory modules, which exhibited complex mosaic structures and contained many antimicrobial resistance loci and associated ARGs. Integration of ARG-containing AGEs into Morganella chromosomes would contribute to the accumulation and dissemination of ARGs in Morganella and enhance the adaption and survival of Morganella under complex and diverse antimicrobial selection pressures. IMPORTANCE This study presents a comprehensive genomic epidemiology analysis on global sequenced Morganella isolates. First, a genome sequence-based species classification scheme for Morganella is established with a higher resolution and accuracy than those of the conventional scheme. Second, the prevalence of accessory genetic elements (AGEs) and associated antimicrobial resistance genes (ARGs) among Morganella isolates is disclosed based on genome sequences. Finally, a detailed sequence comparison of eight groups of 23 AGEs (including 19 Morganella chromosomal AGEs) reveals that Morganella chromosomes have evolved to acquire diverse AGEs harboring different profiles of ARGs and that some of these AGEs harbor large accessory modules that exhibit complex mosaic structures and contain a large number of ARGs. Data presented here provide a deeper understanding of the classification and evolution of Morganella species and also those of ARG-containing AGEs in Morganella at the genomic scale.

Tetramethylpyrazine alleviates diabetes-induced high platelet response and endothelial adhesion via inhibiting NLRP3 inflammasome activation

BACKGROUND

The inflammatory state of diabetes promotes high platelet response and endothelial adhesion, which are the main risk factors for cardiovascular events. Tetramethylpyrazine (TMP) is an amide alkaloid isolated from the traditional Chinese medicine Rhizoma Ligustici Chuanxiong, which has been widely used in the clinical treatment of ischemic cardiovascular disease.

PURPOSE

This study aimed to investigate whether TMP could alleviate diabetes-induced high platelet response and endothelial adhesion and the underlying mechanisms.

METHODS

Type 2 diabetes mellitus (T2DM) rat model was established by high-fat feeding combined with low dose of streptozotocin. Rats in the TMP treatment group were administered with TMP (100 or 200 mg/kg) for 21 days. Cultured human umbilical vein endothelial cells (HUVECs) were stimulated with glucose (5.5 mM) to induce endothelial activation. The NOD-like receptor protein 3 (NLRP3) over- and low-expressing cell models were established via transfection of NLRP3 lentivirus plasmid into HUVECs. INF39 (25 mg/kg), a chemical inhibitor of NLRP3 inflammasome, was used to explore the role of NLRP3 in T2DM associated high platelet response and endothelial adhesion.

RESULTS

TMP effectively improved the prothrombotic phenotypes and inhibited the expression of vascular inflammatory factors and adhesion molecules in T2DM rats. TMP inhibited NLRP3 inflammasome and reduced the adhesion of HUVECs to platelets and monocytes in vitro. Over-expression of NLRP3 blocked the effect of TMP on HUVECs activation and adhesion, while TMP had no effect on NLRP3 low-expressing HUVECs. The NLRP3 inhibitor INF39 produced similar effects of TMP on diabetes-induced high platelet response, endothelial adhesion and vascular inflammation.

CONCLUSION

TMP ameliorates diabetes-induced high platelet response and endothelial adhesion via inhibiting NLRP3 inflammasome activation in T2DM rats, which provide a new basis for the clinical prevention and treatment of diabetes-associated cardiovascular events.

Measurement of Prompt D^{0}, Λ_{c}^{+}, and Σ_{c}^{0,++}(2455) Production in Proton-Proton Collisions at sqrt[s]=13 TeV

The p_{T}-differential production cross sections of prompt D^{0}, Λ_{c}^{+}, and Σ_{c}^{0,++}(2455) charmed hadrons are measured at midrapidity (|y|<0.5) in pp collisions at sqrt[s]=13  TeV. This is the first measurement of Σ_{c}^{0,++} production in hadronic collisions. Assuming the same production yield for the three Σ_{c}^{0,+,++} isospin states, the baryon-to-meson cross section ratios Σ_{c}^{0,+,++}/D^{0} and Λ_{c}^{+}/D^{0} are calculated in the transverse momentum (p_{T}) intervals 2<p_{T}<12 and 1<p_{T}<24  GeV/c. Values significantly larger than in e^{+}e^{-} collisions are observed, indicating for the first time that baryon enhancement in hadronic collisions also extends to the Σ_{c}. The feed-down contribution to Λ_{c}^{+} production from Σ_{c}^{0,+,++} is also reported and is found to be larger than in e^{+}e^{-} collisions. The data are compared with predictions from event generators and other phenomenological models, providing a sensitive test of the different charm-hadronization mechanisms implemented in the models.

Study on Dynamic Progression and Risk Assessment of Metabolic Syndrome Based on Multi-State Markov Model

AIM

Metabolic syndrome (MetS) coexists with the occurrence and even death of cardiovascular disease and diabetes mellitus. It is essential to study the factors in the dynamic progression of MetS in the interest of prevention and control.

PURPOSE

The aim of this study was to analyze the dynamic progression of Mets and explore the potential factors influencing the progression or reversal of MetS.

PATIENTS AND METHODS

This study involved 5581 individuals from two waves of the China Health and Retirement Longitudinal Study: 2011 and 2015. A multistate Markov model containing 4 states (free of metabolic disorder (FMD), mild metabolic disorder (MMD), severe metabolic disorder (SMD) and MetS) was adopted to study the dynamic progression of MetS and its influencing factors.

RESULTS

After follow-up, a total of 2862 cases (50.28% of the total number) had disease state transition. The intensity of transition from MetS to SMD is the same as that from SMD to MMD, and is greater than that from MMD to Mets (0.06 vs 0.05). For the MetS state, a mean of 1/0.08=12.5 years was spent in the MetS state before recovery. The exercise, smoke, drink, BMI level, hyperuricemia had statistically significant effects on progression of MetS status (P<0.05). The obesity or overweight, little exercise, smoke, drink and hyperuricemia increased the risk of forward progression of MetS disease status. There were significant nonmodifiable (age, gender) and modifiable factors (exercise, drink, BMI level, or high HbA1c) associated with reversion of MetS state.

CONCLUSION

The likelihood of progression from MMD to MetS is less likely than that of reversion from MetS to SMD and SMD to MMD. Old females were more resistant to recover from worse states than males. Prevention and intervention measures should be adopted early when MMD or SMD onset occurs.

Measurement of the Cross Sections of Ξ_{c}^{0} and Ξ_{c}^{+} Baryons and of the Branching-Fraction Ratio BR(Ξ_{c}^{0}→Ξ^{-}e^{+}ν_{e})/BR(Ξ_{c}^{0}→Ξ^{-}π^{+}) in pp Collisions at sqrt[s]=13 TeV

The p_{T}-differential cross sections of prompt charm-strange baryons Ξ_{c}^{0} and Ξ_{c}^{+} were measured at midrapidity (|y|<0.5) in proton-proton (pp) collisions at a center-of-mass energy sqrt[s]=13  TeV with the ALICE detector at the LHC. The Ξ_{c}^{0} baryon was reconstructed via both the semileptonic decay (Ξ^{-}e^{+}ν_{e}) and the hadronic decay (Ξ^{-}π^{+}) channels. The Ξ_{c}^{+} baryon was reconstructed via the hadronic decay (Ξ^{-}π^{+}π^{+}) channel. The branching-fraction ratio BR(Ξ_{c}^{0}→Ξ^{-}e^{+}ν_{e})/BR(Ξ_{c}^{0}→Ξ^{-}π^{+})=1.38±0.14(stat)±0.22(syst) was measured with a total uncertainty reduced by a factor of about 3 with respect to the current world average reported by the Particle Data Group. The transverse momentum (p_{T}) dependence of the Ξ_{c}^{0}- and Ξ_{c}^{+}-baryon production relative to the D^{0} meson and to the Σ_{c}^{0,+,++}- and Λ_{c}^{+}-baryon production are reported. The baryon-to-meson ratio increases toward low p_{T} up to a value of approximately 0.3. The measurements are compared with various models that take different hadronization mechanisms into consideration. The results provide stringent constraints to these theoretical calculations and additional evidence that different processes are involved in charm hadronization in electron-positron (e^{+}e^{-}) and hadronic collisions.

The Effect of Salinity on Biofilm Formation and c-di-GMP Production in Vibrio parahaemolyticus

Vibrio parahaemolyticus is a moderately halophilic, salt-requiring organism that exhibits optimal growth at approximately 3% salt. Thus, salinity stress is one of the most important stimuli during its lifecycle. The bacterium possesses a strong ability to form biofilms on surfaces, which are thought to be involved in protecting it from adverse environmental conditions. In the present study, salinity-dependent biofilm formation by V. parahaemolyticus was investigated by combining crystal violet staining, colony morphology, intracellular c-di-GMP quantification and quantitative PCR. The results showed that biofilm formation by V. parahaemolyticus was significantly enhanced in low salinity growth conditions and was affected by incubation time. In addition, low salinity reduced intracellular c-di-GMP degradation in V. parahaemolyticus. Transcription of genes encoding ScrABC and ScrG proteins, which are involved in intracellular c-di-GMP metabolism, was inhibited by low salinity growth conditions. Thus, reduced intracellular c-di-GMP degradation in V. parahaemolyticus in low salinity growth conditions may be mediated by repression of scrG and scrABC transcription. Taken together, these results demonstrated for the first time that salinity regulates biofilm formation and c-di-GMP production in V. parahaemolyticus.

Self-resetting molecular probes for nucleic acids detection enabled by fuel dissipative systems

A once-in-a-century global public health crisis, the COVID-19 pandemic has damaged human health and world economy greatly. To help combat the virus, we report a self-resetting molecular probe capable of repeatedly detecting SARS-CoV-2 RNA, developed by orchestrating a fuel dissipative system via DNA nanotechnology. A set of simulation toolkits was utilized to design the probe, permitting highly consistent signal amplitudes across cyclic detections. Uniquely, full width at half maximum regulated by dissipative kinetics exhibits a fingerprint signal suitable for high confidential identifications of single-nucleotide variants. Further examination on multiple human-infectious RNA viruses, including ZIKV, MERS-CoV, and SARS-CoV, demonstrates the generic detection capability and superior orthogonality of the probe. It also correctly classified all the clinical samples from 55 COVID-19 patients and 55 controls. Greatly enhancing the screening capability for COVID-19 and other infectious diseases, this probe could help with disease control and build a broader global public health agenda.

Λ_{c}^{+} Production and Baryon-to-Meson Ratios in pp and p-Pb Collisions at sqrt[s_{NN}]=5.02 TeV at the LHC

The prompt production of the charm baryon Λ_{c}^{+} and the Λ_{c}^{+}/D^{0} production ratios were measured at midrapidity with the ALICE detector in pp and p-Pb collisions at sqrt[s_{NN}]=5.02  TeV. These new measurements show a clear decrease of the Λ_{c}^{+}/D^{0} ratio with increasing transverse momentum (p_{T}) in both collision systems in the range 2<p_{T}<12  GeV/c, exhibiting similarities with the light-flavor baryon-to-meson ratios p/π and Λ/K_{S}^{0}. At low p_{T}, predictions that include additional color-reconnection mechanisms beyond the leading-color approximation, assume the existence of additional higher-mass charm-baryon states, or include hadronization via coalescence can describe the data, while predictions driven by charm-quark fragmentation processes measured in e^{+}e^{-} and e^{-}p collisions significantly underestimate the data. The results presented in this Letter provide significant evidence that the established assumption of universality (colliding-system independence) of parton-to-hadron fragmentation is not sufficient to describe charm-baryon production in hadronic collisions at LHC energies.

Sustainable Silk-Derived Multimode Carbon Dots

Carbon dots (CDs) are widely studied for years due to their unique luminescent properties and potential applications in many fields. However, aggregation-caused quenching, monotonous emission modes, and unsustainable preparation impose restrictions on their performance and practical applications. Here, this work reports the facile synthesis of sustainable silk-derived multimode emitting CDs with dispersed-state fluorescence (DSF), aggregation-induced fluorescence (AIF), and aggregation-induced room temperature phosphorescence (AIRTP) through radiating sericin proteins in a household microwave oven (800 W, 2.5 min). The structure, luminescent properties, and the mechanism are investigated and discussed. The sericin-derived CDs have graphitized cores and heteroatom-cluster-rich surfaces. The DSF corresponds to the graphitized cores and the AIF origins from the aggregation-induced abundant orbital energy levels on the heteroatom-cluster-rich surfaces. The presence of abundant hydrogen bonds and small gap between the lowest singlet and triplet excited states induces AIRTP. Finally, based on the unique multimode emission of the prepared CDs, their applications in high-performance white-light-emitting diode, information encryption, anti-counterfeiting, and visual humidity sensors are demonstrated.

Experimental Evidence for an Attractive p-ϕ Interaction

This Letter presents the first experimental evidence of the attractive strong interaction between a proton and a ϕ meson. The result is obtained from two-particle correlations of combined p-ϕ⊕ p[over ¯]-ϕ pairs measured in high-multiplicity pp collisions at sqrt[s]=13  TeV by the ALICE Collaboration. The spin-averaged scattering length and effective range of the p-ϕ interaction are extracted from the fully corrected correlation function employing the Lednický-Lyuboshits approach. In particular, the imaginary part of the scattering length vanishes within uncertainties, indicating that inelastic processes do not play a prominent role for the p-ϕ interaction. These data demonstrate that the interaction is dominated by elastic p-ϕ scattering. Furthermore, an analysis employing phenomenological Gaussian- and Yukawa-type potentials is conducted. Under the assumption of the latter, the N-ϕ coupling constant is found to be g_{N-ϕ}=0.14±0.03(stat)±0.02(syst). This work provides valuable experimental input to accomplish a self-consistent description of the N-ϕ interaction, which is particularly relevant for the more fundamental studies on partial restoration of chiral symmetry in nuclear medium.

Biomass-Derived Carbon Materials: Controllable Preparation and Versatile Applications

Biomass-derived carbon materials (BCMs) are encountering the most flourishing moment because of their versatile properties and wide potential applications. Numerous BCMs, including 0D carbon spheres and dots, 1D carbon fibers and tubes, 2D carbon sheets, 3D carbon aerogel, and hierarchical carbon materials have been prepared. At the same time, their structure-property relationship and applications have been widely studied. This paper aims to present a review on the recent advances in the controllable preparation and potential applications of BCMs, providing a reference for future work. First, the chemical compositions of typical biomass and their thermal degradation mechanisms are presented. Then, the typical preparation methods of BCMs are summarized and the relevant structural management rules are discussed. Besides, the strategies for improving the structural diversity of BCMs are also presented and discussed. Furthermore, the applications of BCMs in energy, sensing, environment, and other areas are reviewed. Finally, the remaining challenges and opportunities in the field of BCMs are discussed.

Multiharmonic Correlations of Different Flow Amplitudes in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV

The event-by-event correlations between three flow amplitudes are measured for the first time in Pb-Pb collisions, using higher-order symmetric cumulants. We find that different three-harmonic correlations develop during the collective evolution of the medium when compared to correlations that exist in the initial state. These new results cannot be interpreted in terms of previous lower-order flow measurements since contributions from two-harmonic correlations are explicitly removed in the new observables. A comparison to Monte Carlo simulations provides new and independent constraints for the initial conditions and system properties of nuclear matter created in heavy-ion collisions.

Diversification and prevalence of the quinolone resistance crpP genes and the crpP-carrying Tn6786-related integrative and conjugative elements in Pseudomonas aeruginosa

The quinolone resistance crpP genes can mediate decreased susceptibility to quinolones. However, diversification and prevalence of crpP genes and crpP-carrying integrative and conjugative elements (ICEs) still need to be elucidated. In this study, genome sequencing was conducted for 200 Chinese Pseudomonas aeruginosa isolates, 16 of which were fully sequenced. All the 37 available CrpP variants were collected for phylogenetic analysis, 10 CrpP enzymes were chosen to conduct cloning and antimicrobial susceptibility test, and 22 crpP-carrying Tn6786-related ICEs were selected for detail genetic dissection analysis. Then, typing/nomenclature schemes for crpP variants and crpP-carrying ICEs were established for the first time. The 10 representative CrpP enzymes were confirmed to mediate decreased susceptibility to one to three quinolones. Tn6786-related ICEs displayed high-level diversification in both nucleotide sequences and modular structures. Mainly, massive gene acquisition/loss occurred across the whole genomes of Tn6786-related ICEs. 53.5% (107/200) of the tested clinical P. aeruginosa isolates from China carried crpP genes, which were exclusively located within chromosome-borne Tn6786-related ICEs. The crpP-carrying ICEs were at active stages of evolution and had the high potential to be an important vector for the dissemination of resistance genes besides crpP. The present study furthered the understanding of the bioinformatics and epidemiology of crpP genes and crpP-carrying ICEs.

Prevalence and influencing risk factors of eczema among preschool children in Urumqi city: a cross-sectional survey

Background

Eczema is a chronic inflammatory disease associated with impaired quality of life. We identified indoor environmental risk factors, to provide strong evidence for the prevention and control of eczema in preschool children.

Methods

Using a cross-sectional study with stratified random cluster sampling, we conducted a self-administered questionnaire survey among 8153 parents of children aged 2–8 years in 60 kindergartens in six districts of Urumqi city during August 2019.

Results

Among 8153 preschool children, 12.0% of the children have been diagnosed with eczema. Multivariate logistic regression analysis showed that caesarean section (odds ratio [OR] = 1.18, 95% confidence interval [CI]: 1.03–1.36), being an only child (OR = 1.36, 95% CI: 1.18–1.57), presence of mould or moisture in the mother’s home before pregnancy (OR = 1.53, 95% CI: 1.17–2.00), presence of flies or mosquitoes in the dwelling currently (OR = 1.31, 95% CI: 1.10–1.55), pets kept in the child’s home currently (OR = 1.23, 95% CI: 1.01–1.51), presence of pets during child’s first year (OR = 1.45, 95% CI: 1.14–1.85), and family history of eczema (OR = 3.53, 95% CI: 2.98–4.19) are the risk factors for the development of eczema, whereas ethnicity other than the Han Chinese (OR = 0.77, 95% CI: 0.61–0.96) is a protective factor for eczema.

Conclusion

Preschool children in Urumqi are at a high risk of eczema, particularly those of the Han Chinese ethnicity. Parents should be attentive to the indoor living environment of children and take actions to reduce indoor humidity, pest control and elimination, and avoid raising pets to reduce the risk of development of eczema in children.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-021-02819-5.

Influence of the interaction between parental myopia and poor eye habits when reading and writing and poor reading posture on prevalence of myopia in school students in Urumqi, China

Background

To evaluate the prevalence of myopia in school students in Urumqi, China, and explore the influence of the interaction between parental myopia and poor reading and writing habits on myopia to identify the at-risk population and provide evidence to help school students avoid developing myopia.

Methods

A cross-sectional survey was conducted with 6,883 school students aged 7–20 years in Urumqi in December 2019. The Standard Eye Chart and mydriatic optometry were used to determine whether students had myopia. Falconer’s method was used to calculate the heritability of parental myopia. Multivariate unconditional logistic regression models were used to analyze the risk factors for myopia and the additive and multiplicative interaction of parental myopia and poor reading and writing habits.

Results

After standardizing the age of the 6,883 students, the overall prevalence rate of myopia was 47.50 %. The heritability of parental myopia was 66.57 % for boys, 67.82 % for girls, 65.02 % for the Han group, and 52.71 % for other ethnicities. There were additive interactions between parental myopia and poor reading and writing habits; among them, parental myopia and poor eye habits when reading and writing (the distance between the eyes and book is less than 30 cm when reading and writing, fingers block the sight of one eye while holding the pen, and leaning one’s body when reading and writing; habit 1) increased the risk of myopia by 10.99 times (odds ratio [OR] = 10.99, 95 % confidence interval [CI] = 8.33–14.68), parental myopia and poor reading posture (reading while lying down, walking, or in the car; habit 2) increased the risk of myopia by 5.92 times (OR = 5.92, 95 % CI = 4.84–7.27). There was no multiplicative interaction between parental myopia and habit 1 or habit 2 (OR = 0.69, 95 % CI = 0.44–1.08; OR = 0.89, 95 % CI = 0.66–1.21, respectively).

Conclusion

The prevalence of myopia among students in Urumqi, Xinjiang is relatively high. The risk of developing myopia is affected by parental myopia and poor reading and writing habits. In addition, parental myopia amplifies the harm caused by poor reading and writing habits, thereby increasing the risk of myopia. Students with parents who have myopia should be targeted during myopia prevention efforts.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12886-021-02058-3.

MicroRNA-449 targets histone deacetylase 1 to regulate the proliferation, invasion, and apoptosis of synovial fibroblasts in rheumatoid arthritis

BACKGROUND

Rheumatoid arthritis (RA) is a chronic joint disease. The study aimed to explore the effects of microRNA (miR)-449 and histone deacetylase 1 (HDAC1) on the proliferation, invasion, and apoptosis of synovial fibroblasts in rheumatoid arthritis.

METHODS

Synovial tissue was collected from 20 patients with RA and 20 patients with osteoarthritis (OA) who underwent joint replacement surgery. RA synovial fibroblasts (RASFs) and OA synovial fibroblasts (OASFs) were isolated and cultured. Real-time quantitative PCR was used to detect the expression levels of miR-449 and HDAC1 in synovial tissues and cells. Western blot was performed to detect the cellular expression levels of HDAC1 protein, and apoptosis and invasion-related proteins. The proliferation, invasion, and apoptosis of RASFs were detected by MTT assay, Transwell assay, and flow cytometry. The dual-luciferase reporter gene was used to test the targeting relationship between inflammatory miR-449 and HDAC1.

RESULTS

Compared with normal synovial tissue and OASFs, the levels of HDAC1 messenger RNA in RA synovial tissue and RASF cells were significantly increased (P<0.01), while the expression levels of miR-449 were significantly decreased (P<0.01). The dual-luciferase reporter gene experiment confirmed that miR-449 could specifically bind to the 3' untranslated region of HDAC1 to inhibit its luciferase activity (P<0.05). HDAC1 inhibition or miR-449 overexpression significantly inhibited the proliferation and invasion of RASFs (P<0.001), while inducing their apoptosis (P<0.001). HDAC1 overexpression reversed the biological effects of miR-449 on RASFs (P<0.001).

CONCLUSIONS

miR-449 inhibits the proliferation and invasion of RASFs and induces their apoptosis by targeting HDAC1, thereby exerting a protective effect against RA.

Construction of Robust Cadmium-Free Cu-In-Zn-S Nanocrystals and Polyfluorene Derivatives Hybrid Emissive Layer for Stable Electroluminescent White Light-Emitting Devices

Combination of the merit of inorganic nanocrystals (NCs) and solution-processed conjugated polymer is a convenient strategy to obtain stable and efficient electroluminescent white-light-emitting diodes (el-WLEDs). In this work, an el-WLED was fabricated on the basis of Cd-free Cu-In-Zn-S (CIZS)/ZnS NCs blending with polyfluorene derivative poly[4-(octyloxy)-9,9-diphenylfluoren-2,7-diyl]-co-[5-(octyloxy)-9,9-diphenylfluoren-2,7-diyl] (PODPF), which exhibited a stable white light emission with a color rendering index value of 85. Meanwhile, it had a stable spectrum under high voltage due to the extremely weak energy transfer between PODPF and CIZS/ZnS NCs. To further improve the device performance, PC₉O₄ was used to replace PODPF, which presented better solubility and smoother film-forming properties. Thus, the maximum external quantum efficiency (EQE) of the optimized el-WLED was increased by 221% while maintaining a stable spectrum under high voltage. This work may provide a great foundation on color mixing cadmium-free el-WLEDs.

Soft-Dielectron Excess in Proton-Proton Collisions at sqrt[s]=13 TeV

A measurement of dielectron production in proton-proton (pp) collisions at sqrt[s]=13  TeV, recorded with the ALICE detector at the CERN LHC, is presented in this Letter. The data set was recorded with a reduced magnetic solenoid field. This enables the investigation of a kinematic domain at low dielectron (ee) invariant mass m_{ee} and pair transverse momentum p_{T,ee} that was previously inaccessible at the LHC. The cross section for dielectron production is studied as a function of m_{ee}, p_{T,ee}, and event multiplicity dN_{ch}/dη. The expected dielectron rate from hadron decays, called hadronic cocktail, utilizes a parametrization of the measured η/π^{0} ratio in pp and proton-nucleus collisions, assuming that this ratio shows no strong dependence on collision energy at low transverse momentum. Comparison of the measured dielectron yield to the hadronic cocktail at 0.15<m_{ee}<0.6  GeV/c^{2} and for p_{T,ee}<0.4  GeV/c indicates an enhancement of soft dielectrons, reminiscent of the "anomalous" soft-photon and soft-dilepton excess in hadron-hadron collisions reported by several experiments under different experimental conditions. The enhancement factor over the hadronic cocktail amounts to 1.61±0.13(stat)±0.17(syst,data)±0.34(syst,cocktail) in the ALICE acceptance. Acceptance-corrected excess spectra in m_{ee} and p_{T,ee} are extracted and compared with calculations of dielectron production from hadronic bremsstrahlung and thermal radiation within a hadronic many-body approach.

A review of the functions of G protein-coupled estrogen receptor 1 in vascular and neurological aging

Aging-related diseases, especially vascular and neurological disorders cause huge economic burden. How to delay vascular and neurological aging is one of the insurmountable questions. G protein-coupled estrogen receptor 1 (GPER) has been extensively investigated in recent years due to its multiple biological responses. In this review, the function of GPER in aging-related diseases represented by vascular diseases, and neurological disorders were discussed. Apart from that, activation of GPER was also found to renovate the aging brain characterized by memory decline, but in a manner different from another two nuclear estrogen receptors estrogen receptor (ER)α and ERβ. This salutary effect would be better clarified from the aspects of synaptic inputs and transmission. Furthermore, we carefully described molecular mechanisms underpinning GPER-mediated effects. This review would update our understanding of GPER in the aging process. Targeting GPER may represent a promising strategy in the aging-related disorders.

Phageome-based vaccination and human innate immune modulation could be a useful strategy to control human Coronavirus infections

Human Coronavirus (CoV) infections, including SARS-COV, MERS-COV, and SARS-CoV-2, usually cause fatal lower and upper respiratory tract infections due to exacerbated expression of pro-inflammatory cytokines and chemokines. We aim to summarize different aspects, such as CoV immune evasion mechanisms and host innate immune response to these infections, and their role in pathogenesis. We have also elaborated the up-to-date findings on different vaccine development strategies and progress against CoVs in both humans and non-human models. Most importantly, we have described the Phageome-human immune interaction, its therapeutic usage as anti-viral, anti-inflammatory agent, and implications for multiple vaccine development systems. The data suggest that endogenous phages might play a vital role in eliminating the infection and regulating the body's immune system. Considering the innate-immune-induced pathogenesis against CoVs and the therapeutic aptitude of phageome, we propose that the prophylactic administration of phages and phage-based vaccines could be a useful strategy to control the emerging CoV infections.

Down-Regulation of HBXIP Inhibits Non-Small Cell Lung Cancer Growth and Enhances the Anti-Tumor Immunity of Mice by Reducing NRP-1

OBJECTIVE

Hepatitis B X-interacting protein (HBXIP) interacts with hepatitis B virus X protein to participate in the replication of the hepatitis B virus and carcinogenesis. Cellular growth and metastasis of non-small-cell lung cancer (NSCLC) are repressed by HBXIP inhibition. However, the role and mechanism of HBXIP on NSCLC cell growth remain unknown.

MATERIALS

Expression of HBXIP was assessed by qRT-PCR and Western blot. siRNA targeting HBXIP was applied to detect cell viability and proliferation by MTT and colony formation assays. In vivo tumor growth was assessed, and anti-tumor immunity was determined by flow cytometry. The downstream partners involved in HBXIP-mediated tumorigenesis were detected by Western blot.

RESULTS

Expression of HBXIP and neuropilin1-1 (NRP-1) was higher in NSCLC tissues and cells than in paracancerous tissues and human lung epithelial cells. siRNA-mediated knockdown of HBXIP decreased the cell viability of NSCLC and suppressed proliferation. Protein expression of Lin28B and NRP-1 was reduced by the knockdown of HBXIP, and over-expression of Lin28B attenuated the HBXIP silence-induced decrease of NRP-1. In vivo tumor growth was suppressed by HBXIP silencing, and the knockdown of HBXIP enhanced anti-tumor immunity through the increase of CD4+ and CD8+ T lymphocytes.

CONCLUSION

Down-regulation of HBXIP reduced Lin28B-mediated NRP-1 to suppress NSCLC cell growth and enhance anti-tumor immunity.

Plasmids of novel incompatibility group IncpRBL16 from Pseudomonas species

OBJECTIVES

To dissect genomic features of IncpRBL16 plasmids from Pseudomonas.

METHODS

An extensive genomic comparison was applied to all 17 available sequenced IncpRBL16 plasmids, including 8 sequenced in this study and another 2 sequenced in two of our previous studies.

RESULTS

Conserved IncpRBL16 backbone markers repAIncpRBL16 together with its iterons, parB2-parA, che, pil and ter were present in all 17 plasmids. At least 18 regions or sites across IncpRBL16 genomes exhibited major modular differences, including insertion of accessory modules, deletion of backbone regions surrounding insertion sites and substitution of multiple-gene backbone regions. Ten plasmids carried a sole IncpRBL16 replicon, while exogenous acquisition of an auxiliary replicon (located in an accessory module) besides the primary IncpRBL16 replicon was observed in each of the remaining seven plasmids. The 17 IncpRBL16 plasmids carried at least 71 different accessory modules, notably including Tn1403-related regions, Tn7-family transposons, Tn6571-family transposons, integrative and conjugative elements, and integrative and mobilizable elements. There were a total of 40 known resistance genes, which were involved in resistance to 15 categories of antibiotics and heavy metals, notably including blaIMP-9, blaIMP-45, blaVIM-2, blaDIM-2, blaOXA-246, blaPER-1, aphA and armA.

CONCLUSIONS

Different IncpRBL16 plasmids contain different profiles of accessory modules and thus diverse collections of resistance genes. To the best of our knowledge, this is the first report of fully sequenced blaOXA-246-carrying (p12939-PER) and blaPER-1-carrying (p12939-PER and pA681-IMP) IncpRBL16 plasmids and also that of 14 novel (first identified in this study) and additionally 31 newly named (first designated in this study, but with previously determined sequences) mobile elements.

Chromosomal Integration of Huge and Complex bla NDM-Carrying Genetic Elements in Enterobacteriaceae

In this study, a detailed genetic dissection of the huge and complex bla_NDM-carrying genetic elements and their related mobile genetic elements was performed in Enterobacteriaceae. An extensive comparison was applied to 12 chromosomal genetic elements, including six sequenced in this study and the other six from GenBank. These 12 genetic elements were divided into five groups: a novel IME Tn6588; two related IMEs Tn6523 (SGI1) and Tn6589; four related ICEs Tn6512 (R391), Tn6575 (ICEPvuChnBC22), Tn6576, and Tn6577; Tn7 and its derivatives Tn6726 and 40.7-kb Tn7-related element; and two related IMEs Tn6591 (GIsul2) and Tn6590. At least 51 resistance genes, involved in resistance to 18 different categories of antibiotics and heavy metals, were found in these 12 genetic elements. Notably, Tn6576 carried another ICE Tn6582. In particular, the six bla_NDM-carrying genetic elements Tn6588, Tn6589, Tn6575, Tn6576, Tn6726, and 40.7-kb Tn7-related element contained large accessory multidrug resistance (MDR) regions, each of which had a very complex mosaic structure that comprised intact or residual mobile genetic elements including insertion sequences, unit or composite transposons, integrons, and putative resistance units. Core bla_NDM genetic environments manifested as four different Tn125 derivatives and, notably, two or more copies of relevant Tn125 derivatives were found in each of Tn6576, Tn6588, Tn6589, and 40.7-kb Tn7-related element. The huge and complex bla_NDM-carrying genetic elements were assembled from complex transposition and homolog recombination. Firstly identified were eight novel mobile elements, including three ICEs Tn6576, Tn6577, and Tn6582, two IMEs, Tn6588 and Tn6589, two composite transposons Tn6580a and Tn6580b, and one integron In1718.