Background Dietary pattern analysis is a promising approach to understanding the complex relationship between diet and health. While many statistical methods exist, the literature predominantly focuses on classical methods such as dietary quality scores, principal component analysis, factor analysis, clustering analysis, and reduced rank regression. There are some emerging methods that have rarely or never been reviewed or discussed adequately. Methods This paper presents a landscape review of the existing statistical methods used to derive dietary patterns, especially the finite mixture model, treelet transform, data mining, least absolute shrinkage and selection operator and compositional data analysis, in terms of their underlying concepts, advantages and disadvantages, and available software and packages for implementation. Results While all statistical methods for dietary pattern analysis have unique features and serve distinct purposes, emerging methods warrant more attention. However, future research is needed to evaluate these emerging methods’ performance in terms of reproducibility, validity, and ability to predict different outcomes. Conclusion Selection of the most appropriate method mainly depends on the research questions. As an evolving subject, there is always scope for deriving dietary patterns through new analytic methodologies.

The oxygen vacancy in MnO2 is normally proved as the reactive site for the catalytic ozonation, and acquiring a highly reactive crystal facet with abundant oxygen vacancy by facet engineering is advisable for boosting the catalytic activity. In this study, three facet-engineered α-MnO2 was prepared and successfully utilized for catalytic ozonation toward an odorous CH3SH. The as-synthesized 310-MnO2 exhibited superior activity in catalytic ozonation of CH3SH than that of 110-MnO2 and 100-MnO2, which could achieve 100% removal efficiency for 70 ppm of CH3SH within 20 min. The results of XPS, Raman, H2-TPR, and DFT calculation all prove that the (310) facets possess a higher surface energy than other facets can feature the construction of oxygen vacancies, thus facilitating the adsorption and activate O3 into intermediate peroxide species (O2–/O2 2–) and reactive oxygen species (•O2 –/1O2) for eliminating adjacent CH3SH. In situ diffuse reflectance infrared Fourier transform spectroscopy (in situ DRIFTS) revealed that the CH3SH molecular was chemisorbed on S atom to form CH3S–, which was further converted into intermediate CH3SO3 – and finally oxidized into SO4 2– and CO3 2–/CO2 during the process. Attributed to the deep oxidation of CH3SH on 310-MnO2 via efficient cycling of active oxygen vacancies, the lifetime of 310-MnO2 can be extended to 2.5 h with limited loss of activity, while 110-MnO2 and 100-MnO2 were inactivated within 1 h. This study deepens the comprehension of facet-engineering in MnO2 and presents an efficient and portable catalyst to control odorous pollution.

Elucidation of the molecular events underlying hepatic stellate cell (HSC) activation is an essential step toward understanding the biological properties of HSC and clarifying the potential roles of HSCs in liver fibrosis and other liver diseases, including hepatocellular carcinoma. Highthroughput comparative proteomic analysis based on isobaric tags for relative and absolute quantitation (iTRAQ) labeling combined with online two-dimensional nanoscale liquid chromatography and tandem mass spectrometry (2D nano-LC-MS/MS) were performed on an in vitro HSC activation model to obtain a comprehensive view of the protein ensembles associated with HSC activation. In total, 2,417 proteins were confidently identified (false discovery rate <1%), of which 2,322 proteins were quantified. Compared with quiescent HSCs, 519 proteins showed significant differences in activated HSCs (!3.0-fold). Bioinformatics analyses using Ingenuity Pathway Analysis revealed that the 319 up-regulated proteins represented multiple cellular functions closely associated with HSC activation, such as extracellular matrix synthesis and proliferation. In addition to the well-known markers for HSC activation, such as a-smooth muscle actin and collagen types 1 and 3, some novel proteins potentially associated with HSC activation were identified, while the 200 down-regulated proteins were primarily related to immune response and lipid metabolism. Most intriguingly, the top biological function, top network, and top canonical pathway of down-regulated proteins were all involved in immune responses. The expression and/or biological function of a set of proteins were properly validated, especially Bcl2-associated athanogene 2, BAG3, and B7H3. Conclusion: The present study provided the most comprehensive proteome profile of rat HSCs and some novel insights into HSC activation, especially the suppressed immune response. (HEPATOLOGY 2012;332-349)

Background Apical periodontitis (AP) is essentially an inflammatory disease of microbial etiology primarily caused by infection of the pulp and root canal system. Variation of the bacterial communities caused by AP, as well as their changes responding to dental therapy, are of utmost importance to understand the pathogensis of the apical periodontitis and establishing effective antimicrobial therapeutic strategies. This study aims to uncover the composition and diversity of microbiota associated to the root apex to identify the relevant bacteria highly involved in AP, with the consideration of root apex samples from the infected teeth (with/without root canal treatment), healthy teeth as well as the healthy oral. Methods Four groups of specimens are considered, the apical part of root from diseased teeth with and without root canal treatment, and wisdom teeth extracted to avoid being impacted (tooth healthy control), as well as an additional healthy oral control from biofilm of the buccal mucosa. DNA was extracted from these specimens and the microbiome was examined through focusing on the V3-V4 hypervariable region of the 16S rRNA gene using sequencing on Illumina MiSeq platform. Composition and diversity of the bacterial community were tested for individual samples, and between-group comparisons were done through differential analysis to identify the significant changes. Results We observed reduced community richness and diversity in microbiota samples from diseased teeth compared to healthy controls. Through differential analysis between AP teeth and healthy teeth, we identified 49 OTUs significantly down-regulated as well as 40 up-regulated OTUs for AP. Conclusion This study provides a global view of the microbial community of the AP associated cohorts, and revealed that AP involved not only bacteria accumulated with a high abundance, but also those significantly reduced ones due to microbial infection. Electronic supplementary material The online version of this article (10.1186/s12864-019-5474-y) contains supplementary material, which is available to authorized users.

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