Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathway-based analysis provides a technique, which allows a comprehensive understanding of the molecular mechanisms underlying complex diseases. Extensive studies utilizing the methods and applications for pathway-based analysis have significantly advanced our capacity to explore large-scale omics data, which has rapidly accumulated in biomedical fields. This article is a comprehensive review of the pathway-based analysis methods—the powerful methods with the potential to uncover the biological depths of the complex diseases. The general concepts and procedures for the pathway-based analysis methods are introduced and then, a comprehensive review of the major approaches for this analysis is presented. In addition, a list of available pathway-based analysis software and databases is provided. Finally, future directions and challenges for the methodological development and applications of pathway-based analysis techniques are discussed. This review will provide a useful guide to dissect complex diseases.

No abstract

Purpose Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic lung disease of unknown cause with a variable course. Acute exacerbations of IPF (AE-IPF) is sudden accelerations of the disease or a superimposed idiopathic acute injury significantly reducing lung function. To examine the serum concentrations of Progranulin (PGRN) and activin A in patients with AE-IPF in a pilot study. Methods Twenty-one patients with AE-IPF were compared with 23 patients with stable IPF as a control group. Serum PGRN and activin A levels, arterial blood gas measurements, and lung function were determined in these two groups. Results Peripheral blood PGRN and activin A levels in patients with AE-IPF were 83.7 + 10.0 and 14.2 ± 1.7 ng/ml (mean + SD), respectively; higher than those in the control group 61.0 + 5.8 and 5.8 + 1.0 (p < 0.001). PGRN and activin A levels were significantly negatively correlated with carbon monoxide diffusion capacity r = − 0.857 (p < 0.001) and r = − 0.757 (p < 0.001). Conclusion Progranulin (PGRN) and activin A may be involved in the pathogenesis of AE-IPF. They may be possible markers of disease activity in AE-IPF.

Wetlands are the most biologically diverse ecosystems on Earth. The isolation of Streptomyces strains from wetlands is helpful to study their diversity and functions in such habitats. In this study, six strains of Streptomyces were isolated from the rhizosphere soil of three plant species in Huaxi Wetland of Guiyang and were identified as Streptomyces galilaeus, S. avidinii, S. albogriseolus, S. hydrogenans, S. spororaveus, and S. cellulosae, respectively. The six strains all solubilized phosphate, fixed nitrogen, and produced ACC deaminase and siderophores, and four strains also secreted indole-3-acetic acid. The six strains grew well in the ranges of 0%–3% NaCl, 0%–25% PEG, and pH 5.0–10.0, which showed that the screened strains were tolerant to certain degrees of salinity, drought, and acidic/alkaline pH stress. In addition, the S. avidinii WL3 and S. cellulosae WL9 strains (especially the former) significantly promoted seed germination of mung bean, pepper, and cucumber. A pot experiment further showed that WL3 significantly promoted the growth of cucumber seedlings compared with that of the control, with plant height, root length, lateral root number, and fresh weight increased by 104.99%, 49.99%, 94.12%, and 82.86%, respectively. Thus, strains of six species of Streptomyces with multiple plant growth-promoting characteristics were isolated from the wetland. These results lay a foundation for their potential use as microbial agents and seed-coating treatments.

No abstract

The novel coronavirus disease (COVID-19) broke out worldwide in 2020. The purpose of this paper was to find out the impact of migrant population on the epidemic, aiming to provide data support and suggestions for control measures in various epidemic areas. Generalized additive model was utilized to model the relationship between migrant population and the cumulative number of confirmed cases of COVID-19. The difference of spatial distribution was analyzed through spatial autocorrelation and hot spot analysis. Generalized additive model demonstrated that the cumulative number of confirmed cases was positively correlated with migration index and population density. The predictive results showed that, if no travel restrictions are imposed on the migrant population as usual, this number of COVID-19 would have reached 27,483 (95% CI 16,074, 48,097; the actual number was 23,177). The increase in one city (Jian) would be 577.23% (95% CI 322.73%, 972.73%) compared with the real confirmed cases of COVID-19. The average increase in 73 cities was 85.53% (95% CI 19.53%, 189.81%). Among the migration destinations, the number of cases in cities of Hubei province, Chongqing, and Beijing was relatively high, and there were large-scale highprevalence clusters in eastern Hubei province. Without restrictions on migration, the high prevalence areas in Hubei province and its surrounding areas will be further expanded. The reduced population mobility and population density can greatly slow down the spread of the epidemic. All epidemic areas should suspend the transportation between cities, strictly control the population travel, and decrease the population density, so as to reduce the spread of COVID-19.

Purpose To examine the serum concentrations of Progranulin (PGRN) and activin A in patients with acute exacerbations of idiopathic pulmonary fibrosis (AE-IPF) in a pilot study. Methods Twenty-one patients with AE-IPF were compared with 23 patients with stable idiopathic pulmonary fibrosis (IPF) as a control group. Serum PGRN and activin A levels, arterial blood gas measurements and lung function were determined in these two groups. Students t-test was used to compare the differences in PGRN and activin A levels between the two groups, and Spearman correlation coefficient was used to examine the relationship between serum PGRN and activin A levels with carbon monoxide diffusion capacity in patients with IPF. Results Peripheral blood PGRN and activin A levels in patients with AE-IPF were 83.7+10.0 and 14.2+1.7 ng/ml (mean+SD), respectively, higher than those in the control group 61.0+5.8, and 5.8+1.0 (p<0.001). PGRN and activin A levels were significantly negatively correlated with carbon monoxide diffusion capacity (r=-0.857 p<0.001) and r=-0.757 (p<0.001). Conclusion: PGRN and activin A may be involved in the pathogenesis of AE-IPF. They may be possible markers of activity in AE-IPF.

Background: The novel coronavirus disease (COVID-19) broke out worldwide in 2020. The purpose of this paper was to find out the impact of migrant population on the epidemic, aiming to provide data support and suggestions for control measures in various epidemic areas. Methods: Generalized additive model was utilized to model the relationship between migrant population and the cumulative number of confirmed cases of COVID-19. The difference of spatial distribution was analyzed through spatial autocorrelation and hot spot analysis. Results: Generalized additive model demonstrated that the cumulative number of confirmed cases was positively correlated with migration index and population density. The predictive results showed that if no travel restrictions are imposed on the migrant population as usual, the total cumulative number of confirmed cases of COVID-19 would have reached 27 483 (95% CI: 16 074, 48 097; the actual number was 23 177). The increase in one city (Jian) would be 577.23% (95% CI: 322.73%, 972.73%) compared to the real confirmed cases of COVID-19. The average increase in 73 cities was 85.53% (95% CI: 19.53%, 189.81%). Among the migration destinations, the number of cases in cities of Hubei province, Chongqing and Beijing was relatively high, and there were large-scale high-prevalence clusters in eastern Hubei province. Meanwhile, without restrictions on migration, the high prevalence areas in Hubei province and its surrounding areas will be further expanded. Conclusions: The reduced population mobility and population density can greatly slow down the spread of the epidemic. All epidemic areas should suspend the transportation between cities, comprehensively and strictly control the population travel and decrease the population density, so as to reduce the spread of COVID-19.