Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these ...data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.
Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.
Metals with a high density of nanometre-scale twins have demonstrated simultaneous high strength and good ductility, attributed to the interaction between lattice dislocations and twin boundaries. ...Maximum strength was observed at a critical twin lamella spacing (∼15 nm) by mechanical testing; hence, an explanation of how twin lamella spacing influences dislocation behaviours is desired. Here, we report a transition of dislocation nucleation from steps on the twin boundaries to twin boundary/grain boundary junctions at a critical twin lamella spacing (12-37 nm), observed with in situ transmission electron microscopy. The local stress concentrations vary significantly with twin lamella spacing, thus resulting in a critical twin lamella spacing (∼18 nm) for the transition of dislocation nucleation. This agrees quantitatively with the mechanical test. These results demonstrate that by quantitatively analysing local stress concentrations, a direct relationship can be resolved between the microscopic dislocation activities and macroscopic mechanical properties of nanotwinned metals.
The non-virulent Wolbachia strain wMel and the life-shortening strain wMelPop-CLA, both originally from Drosophila melanogaster, have been stably introduced into the mosquito vector of dengue fever, ...Aedes aegypti. Each of these Wolbachia strains interferes with viral pathogenicity and/or dissemination in both their natural Drosophila host and in their new mosquito host, and it has been suggested that this virus interference may be due to host immune priming by Wolbachia. In order to identify aspects of the mosquito immune response that might underpin virus interference, we used whole-genome microarrays to analyse the transcriptional response of A. aegypti to the wMel and wMelPop-CLA Wolbachia strains. While wMel affected the transcription of far fewer host genes than wMelPop-CLA, both strains activated the expression of some immune genes including anti-microbial peptides, Toll pathway genes and genes involved in melanization. Because the induction of these immune genes might be associated with the very recent introduction of Wolbachia into the mosquito, we also examined the same Wolbachia strains in their original host D. melanogaster. First we demonstrated that when dengue viruses were injected into D. melanogaster, virus accumulation was significantly reduced in the presence of Wolbachia, just as in A. aegypti. Second, when we carried out transcriptional analyses of the same immune genes up-regulated in the new heterologous mosquito host in response to Wolbachia we found no over-expression of these genes in D. melanogaster, infected with either wMel or wMelPop. These results reinforce the idea that the fundamental mechanism involved in viral interference in Drosophila and Aedes is not dependent on the up-regulation of the immune effectors examined, although it cannot be excluded that immune priming in the heterologous mosquito host might enhance the virus interference trait.
In this paper, we derive and analyse a compact difference scheme for a distributed-order time-fractional diffusion-wave equation. This equation is approximated by a multi-term fractional ...diffusion-wave equation, which is then solved by a compact difference scheme. The unique solvability of the difference solution is discussed. Using the discrete energy method, we prove the compact difference scheme is unconditionally stable and convergent. Finally, numerical results are presented to support our theoretical analysis.
Objectives
During the 2019 Coronavirus disease (COVID-19) outbreak, malnutrition may contribute to COVID-19 adverse outcomes. We conducted a clinical epidemiological analysis to investigate the ...association of malnutrition with hospitalized duration in patients with COVID-19.
Design
Retrospective survey study.
Setting
Taikang Tongji (Wuhan) hospital in Wuhan, China.
Participants
139 patients with COVID-19.
Methods
In total, 139 patients with COVID-19 from patients in the Infection Department of Taikang Tongji (Wuhan) hospital from February 2020 to April 2020 were analyzed retrospectively. We used the “Global leadership Initiative on Malnutrition(GLIM)” assessment standard published in 2019 to assess nutritional status. Prolonged hospitalization was lasting more than the median value of the hospitalized days (17 days) in this population.
Results
According to the assessment results of GLIM nutrition assessment, the patients were divided into malnutrition group and normal nutrition group. Compared with the patients in the normal nutrition group, the hospitalization time was longer(15.67±6.26 days versus 27.48±5.04 days, P = 0.001). Kaplan-Meier analysis showed patients with malnutrition were more likely to be hospitalized longer compared with those normal nutrition (mean with 95% confidence interval CI: 28.9127.52–30.30 versus 22.7821.76–23.79, P = 0.001). COX regression analysis showed that malnutrition (hazard ratio HR = 3.773, P for trend = 0.001) was proportional associated with being discharged from hospital delayed.
Conclusion and implications
Present findings suggested that malnutrition contributed to predicting a probability of prolonged hospitalization in patients with COVID-19 infection, to whom extra attentions and precautions should be paid during clinical treatments. Based on the existing results, it is recommended that inpatients with nutritional risk or malnutrition start nutritional support treatment as soon as possible.
Mucosal-Associated Invariant T (MAIT) cells are innate-like T cells characterised by the invariant TCR-chain, Vα7.2-Jα33, and are restricted by MR1, which presents bacterial vitamin B metabolites. ...They are important for antibacterial immunity at mucosal sites; however, detailed characteristics of liver-infiltrating MAIT (LI-MAIT) and their role in biliary immune surveillance remain unexplored.
The phenotype and intrahepatic localisation of human LI-MAIT cells was examined in diseased and normal livers. MAIT cell activation in response to E. coli-exposed macrophages, biliary epithelial cells (BEC) and liver B cells was assessed with/without anti-MR1.
Intrahepatic MAIT cells predominantly localised to bile ducts in the portal tracts. Consistent with this distribution, they expressed biliary tropic chemokine receptors CCR6, CXCR6, and integrin αEβ7. LI-MAIT cells were also present in the hepatic sinusoids and possessed tissue-homing chemokine receptor CXCR3 and integrins LFA-1 and VLA-4, suggesting their recruitment via hepatic sinusoids. LI-MAIT cells were enriched in the parenchyma of acute liver failure livers compared to chronic diseased livers. LI-MAIT cells had an activated, effector memory phenotype, expressed α4β7 and receptors for IL-12, IL-18, and IL-23. Importantly, in response to E. coli-exposed macrophages, liver B cells and BEC, MAIT cells upregulated IFN-γ and CD40 Ligand and degranulated in an MR1-dependent, cytokine-independent manner. In addition, diseased liver MAIT cells expressed T-bet and RORγt and the cytokines IFN-γ, TNF-α, and IL-17.
Our findings provide the first evidence of an immune surveillance effector response for MAIT cells towards BEC in human liver; thus they could be manipulated for treatment of biliary disease in the future.
Curcumin has antioxidant functions, regulates the intestinal microbial composition, and alleviates mycotoxin toxicity. The present study aimed to explore whether curcumin could alleviate ochratoxin A ...(OTA)-induced liver injury via the intestinal microbiota. A total of 720 mixed-sex 1-day-old White Pekin ducklings were randomly assigned into 4 groups: CON (control group, without OTA), OTA (fed a diet with 2 mg/kg OTA), CUR (ducks fed a diet with 400 mg/kg curcumin), and OTA + CUR (2 mg/kg OTA plus 400 mg/kg curcumin). Each treatment consisted of 6 replicates and 30 ducklings per replicate. Treatment lasted for 21 D. Results were analyzed by a two-tailed Student t test between 2 groups. Our results demonstrated that OTA treatment had the highest serum low-density lipoprotein (LDL) level among 4 groups. Compared with OTA group, OTA + CUR decreased serum LDL level (P < 0.05). OTA decreased liver catalase (CAT) activity in ducks (P < 0.05), while addition of curcumin in OTA group increased liver CAT activity (P < 0.05). 16S ribosomal RNA sequencing suggested that curcumin increased the richness indices (ACE index) and diversity indices (Simpson index) compared with OTA group (P < 0.05) and recovered the OTA-induced alterations in composition of the intestinal microbiota. Curcumin supplementation relieved the decreased abundance of butyric acid producing bacteria, including blautia, butyricicoccus, and butyricimonas, induced by OTA (P < 0.05). OTA also significantly influenced the metabolism of the intestinal microbiota, such as tryptophan metabolism and glyceropholipid metabolism. Curcumin could alleviate the upregulation of oxidative stress pathways induced by OTA. OTA treatment also increased SREBP-1c expression (P < 0.05). The curcumin group had the lowest expression of FAS and PPARG mRNA (P < 0.05) and the highest expression of NRF2 and HMOX1 mRNA. These results indicated that curcumin could alleviate OTA-induced oxidative injury and lipid metabolism disruption by modulating the cecum microbiota.
In this study, an integrated model (PORO-WSSI II) for wave–seabed–structure interactions (WSSI) is developed by combining (i) the Volume-Averaged Reynolds-Averaged Navier–Stokes (VARANS) equations ...for wave motions in a fluid domain and the porous media flows in porous structures, and (ii) the dynamic Biot's equations for a porous elastic seabed. The effects of the porous flow in seabed and marine structures, and the fluid exchange at the interface between the fluid domain and solid domain on wave characteristics are considered. The finite difference two-step projection method and the forward time difference method are adopted to solve the VARANS equations. The volume of fluid (VOF) method is applied to track water free-surface. The finite element method and the Generalized Newmark method are respectively adopted for the space discretization and time discretization of the dynamic Biot's equations. A one-way integrating method is developed to integrate the VARANS equations with the dynamic Biot's equations. Several experimental data available in the literature are used to validate the integrated model. An overall agreement between the numerical results and the experiment data indicates that the integrated model developed for the WSSI problem is highly reliable. The integrated model is then applied to investigate the dynamic response of a large-scale composite breakwater on a seabed, and the mechanism of WSSI. Numerical results indicate that there are intensive fluid exchanges between the water body and the seabed and strong seepage forces in the seabed under the ocean wave loading. The excessive upward seepage force leads to the liquefaction of the seabed in the region under wave trough. There is a liquefaction zone in the seabed close to the bottom corner of the rubble mound, which may lead to foundation instability of the composite breakwater. The parametric study indicates that the wave characteristics have a significant impact on the liquefaction properties (depth, width and area).
► We proposed an integrated model for wave–seabed–structure interactions. ► Pre-consolidation is considered in the new model, which is important for prediction of liquefaction. ► Numerical results show the applicability of Biot's dynamic poro-elastic model in the rubble mound.
Vδ2
T cells form the predominant human γδ T-cell population in peripheral blood and mediate T-cell receptor (TCR)-dependent anti-microbial and anti-tumour immunity. Here we show that the Vδ2
...compartment comprises both innate-like and adaptive subsets. Vγ9
Vδ2
T cells display semi-invariant TCR repertoires, featuring public Vγ9 TCR sequences equivalent in cord and adult blood. By contrast, we also identify a separate, Vγ9
Vδ2
T-cell subset that typically has a CD27
CCR7
CD28
IL-7Rα
naive-like phenotype and a diverse TCR repertoire, however in response to viral infection, undergoes clonal expansion and differentiation to a CD27
CD45RA
CX
CR1
granzymeA/B
effector phenotype. Consistent with a function in solid tissue immunosurveillance, we detect human intrahepatic Vγ9
Vδ2
T cells featuring dominant clonal expansions and an effector phenotype. These findings redefine human γδ T-cell subsets by delineating the Vδ2
T-cell compartment into innate-like (Vγ9
) and adaptive (Vγ9
) subsets, which have distinct functions in microbial immunosurveillance.
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