Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance

Abstract Background Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis. Results Phylogenetic analysis revealed three major clusters and three singletons, among which close relationship between several strains was discovered, regardless of their host and niches. The “open” genomes with diversity of accessory and strain-specific genomes took advantage towards diversity environments. The purifying selection pressure was the main force on genome evolution, especially in conservative genes. Only 53 gene families were under positive selection pressure. Phenotypic resistance analysis revealed 21 strains were classified as multi-drug resistance (MDR). Ten types of antibiotic resistance genes and two heavy metal resistance operons were discovered in S. xiamenensis. Mobile genetic elements and horizontal gene transfer increased genome diversity and were closely related to MDR strains. S. xiamenensis carried a variety of virulence genes and macromolecular secretion systems, indicating their important roles in pathogenicity and adaptability. Type IV secretion system was discovered in 15 genomes with various sequence structures, indicating it was originated from different donors through horizontal gene transfer. Conclusions This study provided with a detailed insight into the changes in the pan-genome of S. xiamenensis, highlighting its capability to acquire new mobile genetic elements and resistance genes for its adaptation to environment and pathogenicity to human and animals

Trust-aware detection of malicious users in dating social networks

Online dating is an increasingly thriving business which boosts billion-dollar revenues and attracts users in the tens of millions. Despite its popularity, internet dating is not exempt from the concerns about privacy and trust posed by the revelation of potentially sensitive data as well as the exposure to self-reported (and hence potentially distorted) information. The increasing popularity of online dating networks leads to an increase in security concerns and challenges, as well as harmful actions and attacks, such as creating fake accounts, phishing on these networks. To maintain the safety of legitimate online dating users, it is critical to recognize and isolate criminal people as soon as possible. However, researchers concerning malicious user detection in dating social networks are merely a few. To address some key challenges in this space, we propose a trust-aware detection framework to detect malicious users based on different kinds of data from a real dating site. In particular, we develop a user trust model to distinguish between malicious and legitimate users. Furthermore, we propose a novel data-balancing method to improve the recall rate of malicious user detection. Extensive experiments have been conducted over real-world datasets. The results show that the proposed approach yields a precision of up to 59.16% and a recall rate of up to 73%, which is significantly higher than other baseline algorithms. © 2014 IEEE

Mechanical Responses of Curved Pipe Corssing Mining Subsidence Area

The deformation of the curved pipeline in the mining subsidence area may be different from the ordinary straight pipeline. Curved pipeline is prone to large deformation in the mining subsidence area, which may cause pipeline accidents. Thus, it is of great importance to investigate the mechanical properties of the curved pipeline in the mining subsidence area. The numerical simulation model of pipeline-soil coupling was established by the nonlinear numerical simulation method in this study. The mechanical responses of the curved pipeline under the stratum settlement, collapse, and suspension are investigated. The results show that when the settlement area is located below the curved section of the pipeline, the maximum stress is in the middle of the curved section, there will be more high stress areas when the curved angle larger. When the settlement area is located below the half curved part and half straight part of the pipeline, the high stress area of the pipeline is located at the end of the curved section. The stress and displacement increase with the increase of angle in both cases, but the maximum stress in pipeline is not reached the yield strength. Whether the collapse interface is located in the middle of the curved section or at both ends of the curved section, the high stress area occurs near the collapse interface, the large curved angle of the pipeline is prone to generate large high stress area and produce large plastic strain, and the cross section of the pipeline has a tendency to squeeze to one side. For the suspended curved pipeline, the stress, plastic strain and displacement of the suspended curved pipeline increase with the increase of suspended length and curved angle

Additional file 1 of Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance

Supplementary Material 1

Sedimentary Environment, Tectonic Setting, and Uranium Mineralization Implications of the Yimin Formation, Kelulun Depression, Hailar Basin, China

The sandstone-type uranium deposit of the Kelulun Depression is the first industrially valuable uranium deposit discovered in the Hailar Basin. This study performed a systematic examination of 17 sandstone samples from the Yimin Formation in the Kelulun Depression based on various analytical techniques. The findings of the current study were synthesized with previous research to investigate the impact of the redox conditions and the tectonic background of the source area, as well as the paleoclimatic evolution of the Yimin Formation on uranium mineralization. The elemental Mo, U/Th, V/Cr, Ni/Co, and V/(V + Ni) ratios indicate that the paleowater was in an oxygen-rich environment during the deposition of the Yimin Formation. Additionally, the C-value, Sr/Cu, Al2O3/MgO, and Rb/Sr ratios indicate that the Yimin Formation was formed in a paleoclimate characterized by arid-to-semi-arid conditions. The geochemical characteristics of the observed elements indicated that the sediment source of the Yimin Formation was mainly felsic rocks from the upper continental crust, the weathering of the rock was weak, and the tectonic background was a passive continental margin. Coffinite is distributed in the form of cementation and stellates within or around pyrite crystals, and uranium-titanium oxide is mostly distributed in an irregular granular distribution in the biotite cleavage fractures of the study area. In summary, the findings of this study reveal that the tectonic settings, provenance, uranium source, paleoclimate, and oxygen-rich paleowater of the Yimin Formation have important geological significance for the large-scale uranium mineralization of the Kelulun Depression

DataSheet_1_Investigating the influence of breastfeeding on asthma in children under 12 years old in the UK Biobank.xlsx

BackgroundChildhood-onset asthma (COA) has become a major and growing problem worldwide and imposes a heavy socioeconomic burden on individuals and families; therefore, understanding the influence of early-life experiences such as breastfeeding on COA is of great importance for early prevention.ObjectivesTo investigate the impact of breastfeeding on asthma in children under 12 years of age and explore its role at two different stages of age in the UK Biobank cohort.MethodsA total of 7,157 COA cases and 158,253 controls were obtained, with information regarding breastfeeding, COA, and other important variables available through questionnaires. The relationship between breastfeeding and COA were examined with the logistic regression while adjusting for available covariates. In addition, a sibling analysis was performed on 398 pairs of siblings to explain unmeasured family factors, and a genetic risk score analysis was performed to control for genetic confounding impact. Finally, a power evaluation was conducted in the sibling data.ResultsIn the full cohort, it was identified that breastfeeding had a protective effect on COA (the adjusted odds ratio (OR)=0.875, 95% confidence intervals (CIs): 0.831~0.922; P=5.75×10-7). The impact was slightly pronounced in children aged 6-12 years (OR=0.852, 95%CIs: 0.794~0.914, P=7.41×10-6) compared to those aged under six years (OR=0.904, 95%CIs: 0.837~0.975, P=9.39×10-3), although such difference was not substantial (P=0.266). However, in the sibling cohort these protective effects were no longer significant largely due to inadequate samples as it was demonstrated that the power was only 23.8% for all children in the sibling cohort under our current setting. The protective effect of breastfeeding on COA was nearly unchanged after incorporating the genetic risk score into both the full and sibling cohorts.ConclusionsOur study offered supportive evidence for the protective effect of breastfeeding against asthma in children less than 12 years of age; however, sibling studies with larger samples were warranted to further validate the robustness our results against unmeasured family confounders. Our findings had the potential to encourage mothers to initiate and prolong breastfeeding.</p

A Novel Cryptococcal Meningitis Therapy: The Combination of Amphotericin B and Posaconazole Promotes the Distribution of Amphotericin B in the Brain Tissue

The deficient brain tissue distribution of amphotericin B (AMPB) seriously restricts its treatment for the clinical efficacy of cryptococcus neoformans meningitis (CNM). We strive to develop a tactic to increase its concentration in brain tissue. We aimed to investigate whether the combination of AMPB and posaconazole (POS) could be more effective in the treatment of CNM and to elucidate its potential mechanisms. HPLC analysis was used to analyze the concentration of AMPB in mouse serum, brain tissue, and BCECs cells. Schrodinger molecular docking, in vitro plasma balance dialysis, and ultrafiltration analysis were performed to evaluate the combinative effect of AMPB and POS with serum albumin and POS on AMPB plasma protein binding. H&E staining and colonization culture experiment of CN were employed to assess the effect of POS on the efficacy of AMPB. POS + AMPB significantly reduced the concentration of plasma total AMPB and increased its concentration in the brain tissue. However, the P-gp inhibitor zosuquidar, BCRP inhibitor Ko143, and a common inhibitor of both, elacridar, had no significant effect on its concentration. Molecular docking, balance dialysis, and ultrafiltration analysis showed that AMPB and POS had potential binding properties to serum albumin. Meanwhile, 4 and 8 μg/mL POS could significantly increase the concentration of free AMPB in plasma. POS and three inhibitors all had no significant effect on the uptake of AMPB by BCECs, but serum albumin had. The therapeutic effect of CNM in mice was confirmed that AMPB and AMPB+POS could restrain the infiltration of neutrophils and lymphocytes in cortical neurons and improve the bleeding and markedly inhibit the proliferation of CN. Collectively, we propose that POS competitively binds to the plasma protein sites of AMPB, thereby increasing its level in the brain tissue. Meanwhile, POS could enhance the efficacy of AMPB in the treatment of CNM, which may be independent of P-gp and BCRP proteins