Analyzing moisture-heat coupling in a wheat-soil system using data-driven vector autoregression model
Soil temperature and moisture have a close relationship, the accurate controlling of which is important for crop growth. Mechanistic models built by previous studies need exhaustive parameters and seldom consider time stochasticity and lagging effect. To circumvent these problems, this study designed a data-driven stochastic model analyzing soil moisture-heat coupling. Firstly, three vector autoregression models are built using hourly data on soil moisture and temperature at the depth of 10, 30, and 90 cm. Secondly, from impulse response functions, the time lag and intensity of two variables’ response to one unit of positive shock can be obtained, which describe the time length and strength at which temperature and moisture affect each other, indicating the degree of coupling. Thirdly, Granger causality tests unfold whether one variable’s past value helps predict the other’s future value. Analyzing data obtained from Shangqiu Experiment Station in Central China, we obtained three conclusions. Firstly, moisture’s response time lag is 25, 50, and 120 h, while temperature’s response time lag is 50, 120, and 120 h at 10, 30, and 90 cm. Secondly, temperature’s response intensity is 0.2004, 0.0163, and 0.0035 °C for 1% variation in moisture, and moisture’s response intensity is 0.0638%, 0.0163%, and 0.0050% for 1 °C variation in temperature at 10, 30, and 90 cm. Thirdly, the past value of soil moisture helps predict soil temperature at 10, 30, and 90 cm. Besides, the past value of soil temperature helps predict soil moisture at 10 and 30 cm, but not at 90 cm. We verified this model by using data from a different year and linking it to soil plant atmospheric continuum model.
Feng et al. (2019) Analyzing moisture-heat coupling in a wheat-soil system using data-driven vector autoregression model. PeerJ 7:e7101 https://doi.org/10.7717/peerj.7101
A comparison of impact and risk assessment methods based on the IMO Guidelines and EU invasive alien species risk assessment frameworks
A comparative analysis of two risk assessment (RA) frameworks developed to support the implementation of the international Ballast Water Management Convention (BWMC) and European Regulation on Invasive Alien Species (IAS) was performed. This analysis revealed both differences and similarities between the IMO Risk Assessment Guidelines (IMO, 2007) and EU Regulation supplement on RA of IAS (EU, 2018) in RA approaches, key principles, RA components and categories of IAS impacts recommended for assessment. The results of this analysis were used to produce a common procedure for the evaluation of the bioinvasion risk and impact assessment methods intended to support international, regional and/or national policy on IAS. The procedure includes a scoring scheme to assess compliance with the key principles, RA components and categories of bioinvasion impacts taken into account by the methods. In these methods the categories of impacts on human health and economy are underrepresented comparing with impacts on environment.
Srėbalienė et al. (2019) A comparison of impact and risk assessment methods based on the IMO Guidelines and EU invasive alien species risk assessment frameworks. PeerJ 7:e6965 https://doi.org/10.7717/peerj.6965
In vitro performance in cotton plants with different genetic backgrounds: the case of Gossypium hirsutum in Mexico, and its implications for germplasm conservation
One of the best ex situ conservation strategies for wild germplasm is in vitro conservation of genetic banks. The success of in vitro conservation relies heavily on the micropropagation or performance of the species of interest. In the context of global change, crop production challenges and climate change, we face a reality of intensified crop production strategies, including genetic engineering, which can negatively impact biodiversity conservation. However, the possible consequences of transgene presence for the in vitro performance of populations and its implications for biodiversity conservation are poorly documented. In this study we analyzed experimental evidence of the potential effects of transgene presence on the in vitro performance of Gossypium hirsutum L. populations, representing the Mexican genetic diversity of the species, and reflect on the implications of such presence for ex situ genetic conservation of the natural variation of the species. We followed an experimental in vitro performance approach, in which we included individuals from different wild cotton populations as well as individuals from domesticated populations, in order to differentiate the effects of domestication traits dragged into the wild germplasm pool via gene flow from the effects of transgene presence. We evaluated the in vitro performance of five traits related to plant establishment (N = 300): propagation rate, leaf production rate, height increase rate, microbial growth and root development. Then we conducted statistical tests (PERMANOVA, Wilcoxon post-hoc tests, and NMDS multivariate analyses) to evaluate the differences in the in vitro performance of the studied populations. Although direct causality of the transgenes to observed phenotypes requires strict control of genotypes, the overall results suggest detrimental consequences for the in vitro culture performance of wild cotton populations in the presence of transgenes. This provides experimental, statistically sound evidence to support the implementation of transgene screening of plants to reduce time and economic costs in in vitro establishment, thus contributing to the overarching goal of germplasm conservation for future adaptation.
Hernández-Terán et al. (2019) In vitro performance in cotton plants with different genetic backgrounds: the case of Gossypium hirsutum in Mexico, and its implications for germplasm conservation. PeerJ 7:e7017 https://doi.org/10.7717/peerj.7017
Variations in gut bacterial communities of hooded crane (Grus monacha) over spatial-temporal scales
Background Microbes have been recognized as important symbionts to regulate host life. The animal gut harbors abundance and diverse bacteria. Numerous internal and external factors influence intestinal bacterial communities, including diet, seasonal fluctuations and habitat sites. However, the factors that influence the gut bacterial communities of wild bird is poorly characterized. Methods By high-throughput sequencing and statistical analysis, we investigated the variations in gut bacterial communities of the hooded cranes at three wintering stages in Caizi (CZL) and Shengjin Lake (SJL), which are two shallow lakes in the middle and lower Yangtze River floodplain. Results Our results revealed significant differences in gut bacterial community structure and diversity among different sampling sites and wintering stages. Seasonal changes have a significant impact on the gut microbe composition of hooded cranes in the two lakes. ANOSIM analysis demonstrated that the samples in CZL had greater differences in the gut bacterial composition than that in SJL. Our data showed strong evidence that the host’s gut filtering might be an important factor in shaping bacterial community according to mean nearest taxon distance (MNTD). The PICRUSt analysis showed that the predicted metagenomes associated with the gut microbiome were carbohydrate metabolism, amino acid metabolism and energy metabolism over the entire wintering period at the two lakes. Conclusions The results demonstrated that both seasonal changes and habitat sites have significant impact on the gut bacterial communities of hooded cranes. In addition, predictive function of gut microbes in hooded cranes varied over time. These results provide new insights into the gut microbial community of the cranes, which serves as a foundation for future studies.
Dong et al. (2019) Variations in gut bacterial communities of hooded crane (Grus monacha) over spatial-temporal scales. PeerJ 7:e7045 https://doi.org/10.7717/peerj.7045
Stoichiometric ratios support plant adaption to grazing moderated by soil nutrients and root enzymes
Background Vegetation succession is one of the major driving processes of grassland degradation. Stoichiometry significantly contributes to vegetation dynamics. However, a knowledge gap exists in how soil nutrients and root enzymes influence the stoichiometric ratio to affect vegetation dynamics. Methods To address these questions, we selected a dominant species (Leymus chinensis (Trin.) Tzvel.) and a degraded-dominant species (Artemisia frigida Willd.) under different management regimes (enclosure and grazing) on the Inner Mongolia steppe. We measured (i) plant nutrient concentrations, (ii) root enzymes and (iii) soil nutrients to investigate how the selected plant species responded to grazing. Results The results show that: (i) N and P concentrations and the C:N:P ratio in different organs are significantly affected by grazing, and there is variation in the plant species’ response. Grazing significantly increased N and P in the leaves and stems of L. chinensis and the stems and roots of A. frigida. (ii) Grazing significantly increased the activities of glutamine synthase but decreased the activities of acid phosphatase in L. chinensis. The nitrate reductase and acid phosphatase activities significantly increased in A. frigida under grazing conditions. (iii) Grazing decreased the total nitrogen, total phosphorus, and available nitrogen, but increased the available phosphorus in the soil. Conclusion We conclude that A. frigida is better adapted to grazing than L. chinensis, possibly because of its relatively increased stem and root growth, which enhance population expansion following grazing. Conversely, L. chinensis showed increased leaf and stem growth, but suffered nutrient and biomass loss as a result of excessive foraging by livestock, which severely affected its ability to colonize. Root enzymes coupled with soil nutrients can regulate plant nutrients and stoichiometric ratios as an adaptive response to grazing. Thus, we demonstrated that stoichiometric ratios allow species to better withstand grazing disturbances. This study provides a new understanding of the mechanisms involved in grazing-resistance within a plant-soil system.
Ma et al. (2019) Stoichiometric ratios support plant adaption to grazing moderated by soil nutrients and root enzymes. PeerJ 7:e7047 https://doi.org/10.7717/peerj.7047
Genome-wide analysis of the WRKY gene family in drumstick (Moringa oleifera Lam.)
WRKY proteins belong to one of the largest families of transcription factors. They have important functions in plant growth and development, signal transduction and stress responses. However, little information is available regarding the WRKY family in drumstick (Moringa oleifera Lam.). In the present study, we identified 54 MoWRKY genes in this species using genomic data. On the basis of structural features of the proteins they encode, the MoWRKY genes were classified into three main groups, with the second group being further divided into five subgroups. Phylogenetic trees constructed from the sequences of WRKY domains and overall amino acid compositions derived from drumstick and Arabidopsis were similar; the results indicated that the WRKY domain was the main evolutionary unit of WRKY genes. Gene structure and conserved motif analysis showed that genes with similar structures and proteins with similar motif compositions were usually clustered in the same class. Selective pressure analysis indicated that although neutral evolution and positive selection have happened in several MoWRKY genes, most have evolved under strong purifying selection. Moreover, different subgroups had evolved at different rates. The levels of expression of MoWRKY genes in response to five different abiotic stresses (salt, heat, drought, H2O2, cold) were evaluated by reverse transcription polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR), with the results indicating that these genes had different expression levels and that some may be involved in abiotic stress responses. Our results will provide a foundation for cloning genes with specific functions for use in further research and applications.
Zhang et al. (2019) Genome-wide analysis of the WRKY gene family in drumstick (Moringa oleifera Lam.). PeerJ 7:e7063 https://doi.org/10.7717/peerj.7063
Prognosis predictive value of the Oxford Acute Severity of Illness Score for sepsis: a retrospective cohort study
Background The Oxford Acute Severity of Illness Score (OASIS) has shown fair prognosis predictive value in critically ill patients, but its predictive value has not been assessed in septic patients. Objective The aim of this study was to evaluate the performance of the OASIS for the assessment of mortality in septic patients, especially when compared with the Sepsis-related Organ Failure Assessment (SOFA) score. Methods A retrospective cohort study was conducted using data from a public database and septic patients were identified using the Sepsis-3 criteria. The primary outcome was hospital mortality. Data were mainly analyzed using multivariable logistic regression and receiver operating characteristic (ROC) curves. Sensitive analyses were performed in patients with an ICD-9-CM code for sepsis and ROC curves analyses were also conducted in septic patients stratified by the Simplified Acute Physiology Score (SAPS) II as subgroup analyses. Results A total of 10,305 septic patients were included. The OASIS was found to be significantly associated with hospital mortality (odds ratio 1.07 per one-point increase, 95% confidence interval [1.06–1.08]), while ROC curves analyses showed the discriminatory power of the OASIS for hospital mortality was statistically significantly lower than that of the SOFA score (area under the ROC curve: 0.652 vs 0.682, p < 0.001). Results of sensitive analyses were consistent, but the significant difference existed only when the SAPS II was higher than 50 according to results of the subgroup analyses. Conclusions The OASIS might serve as an initial predictor of clinical outcomes for septic patients, but one should be circumspect when it is applied to severer patients.
Chen et al. (2019) Prognosis predictive value of the Oxford Acute Severity of Illness Score for sepsis: a retrospective cohort study. PeerJ 7:e7083 https://doi.org/10.7717/peerj.7083
Global transcriptomic analysis identifies SERPINE1 as a prognostic biomarker associated with epithelial-to-mesenchymal transition in gastric cancer
Background The plasminogen activation system plays a pivotal role in regulating tumorigenesis. In this work, we aim to identify key regulators of plasminogen activation associated with tumorigenesis and explore potential mechanisms in gastric cancer (GC). Methods Gene profiling datasets were extracted from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were screened for and obtained by the GEO2R tool. The Database for Annotation, Visualization and Integrated Discovery was used for GO and KEGG enrichment analysis. Gene set enrichment analysis (GSEA) was performed to verify molecular signatures and pathways among The Cancer Genome Atlas or GEO datasets. Correlations between SERPINE1 and markers of epithelial-to-mesenchymal transition (EMT) were analyzed using the GEPIA database and quantitative real-time PCR (qRT-PCR). Interactive networks of selected genes were built by STRING and Cytoscape software. Finally, selected genes were verified with the Kaplan–Meier (KM) plotter database. Results A total of 104 overlapped upregulated and 61 downregulated DEGs were obtained. Multiple GO and KEGG terms associated with the extracellular matrix were enriched among the DEGs. SERPINE1 was identified as the only regulator of angiogenesis and the plasminogen activator system among the DEGs. A high level of SERPINE1 was associated with a poor prognosis in GC. GSEA analysis showed a strong correlation between SERPINE1 and EMT, which was also confirmed with the GEPIA database and qRT-PCR validation. FN1, TIMP1, MMP2, and SPARC were correlated with SERPINE1.The KM plotter database showed that an overexpression of these genes correlated with a shorter survival time in GC patients. Conclusions In conclusion, SERPINE1 is a potent biomarker associated with EMT and a poor prognosis in GC. Furthermore, FN1, TIMP1, MMP2, and SPARC are correlated with SERPINE1 and may serve as therapeutic targets in reversing EMT in GC.
Xu et al. (2019) Global transcriptomic analysis identifies SERPINE1 as a prognostic biomarker associated with epithelial-to-mesenchymal transition in gastric cancer. PeerJ 7:e7091 https://doi.org/10.7717/peerj.7091
Association between VDR gene FokI polymorphism and renal function in patients with IgA nephropathy
Background Studies have shown that the occurrence and development of IgA nephropathy (IgAN) are genetically susceptible, but the relationship between vitamin D receptor (VDR) gene polymorphisms and renal function in IgAN patients is unclear. Methods We investigated the relationship between VDR FokI (rs2228570) single nucleotide polymorphism (SNP) and renal function and related clinicopathologic parameters in IgAN patients. Clinical and pathological data of 282 IgAN patients treated at the First Affiliated Hospital of Guangxi Medical University were collected, and FokI genotypes were determined by PCR and direct sequencing. Patients were divided into the renal dysfunction group and normal renal function (control) group by estimated glomerular filtration rate (eGFR) and serum creatinine level. Results Frequencies of TT genotype and T allele in the renal dysfunction group were higher than those of the control group. Blood urea nitrogen, serum phosphorus (P), proportions of mesangial cell proliferation, interstitial fibrosis/tubular atrophy and crescents in T allele carriers were higher than those in non-T allele carriers, while eGFR and 25-Hydroxyvitamin D3 were lower in T allele carriers than non-T allele carriers. Multiple linear regression analysis showed that eGFR was affected by FokI genotypes in IgAN patients. Logistics regression analysis showed that middle and elderly age, elevated P, intact parathyroid hormone and TT genotype were independent risk factors for renal dysfunction in IgAN patients; the odds ratio of carrying the TT genotype was as high as 84.77 (P < 0.05 for all). Conclusions IgA nephropathy patients carrying the VDR FokI TT genotype have an increased risk of renal dysfunction. VDR FokI SNP is closely related to renal function, calcium-phosphate metabolism, and related pathological damage in IgAN patients.
Mo et al. (2019) Association between VDR gene FokI polymorphism and renal function in patients with IgA nephropathy. PeerJ 7:e7092 https://doi.org/10.7717/peerj.7092
Age-related kinematic performance should be considered during fast head-neck rotation target task in individuals aged from 8 to 85 years old
Kinematic behavior during fast cervical rotations is a useful parameter for assessing sensorimotor control performances in neck-pain patients. However, the influence of age in asymptomatic individuals from children to older people still needs to be explored. Our aim was to assess the impact of age on sensorimotor control performance of the head-neck with execution time and kinematic variables (time of task, mean speed/acceleration/deceleration, overshoots (OSs), minimum/maximum speed) during standardized fast rotation target task using the DidRen Laser test. A total of 80 volunteers were stratified in four different age-groups: Children (8–14 years): n = 16; Young Adults (18–35 years): n = 29; Old Adults (36–64 years): n = 18; Seniors (65–85 years): n = 17. Results showed that to perform the test, Children were slower (69.0 (60.6–87.3)s) compared to Young Adults (49.6 (45.6–55.6)s) with p < 0.001, and Old Adults (51.7 (48.4–55.8)s) with p < 0.001. It was also slower in Seniors (57 (52.3–67.6)s) compared to Young Adults with p < 0.013. Mean speed was slower in Children (9.4 ± 2.3 °s−1) and Seniors (10.6 ± 2.4 °s−1) compared to Young Adults (13.7 ± 1.9 °s−1) with p < 0.001 and Old Adults (13.3 ± 2.4 °s−1) with p < 0.001. Mean acceleration was slower for Children (8.4(7.6–10.2) °s−2) compared to Young Adults (11.1 (8.8–15.3) °s−2) with p < 0.016, and Old Adults (12.0(8.4–15.3) °s−2) with p < 0.015. Mean deceleration was slower for Children (−1.9(−2.6–1.4) °s−2) compared to Young Adults (−2.9(−3.7–2.5) °s−2) with p < 0.001 and Old Adults (−3.2(−3.7–2.3) °s−2) with p < 0.003. The DidRen Laser test allows us to discriminate age-specific performances for mean speed, acceleration and deceleration. Seniors and Children needed to be slower to become as precise as Young Adults and Old Adults. No difference was observed for OSs which assesses accuracy of movement. Age should therefore be considered as a key parameter when analyzing execution time and kinematic results during DidRen Laser test. These normative data can therefore guide clinicians in the assessment of subjects with neck pain.
Hage et al. (2019) Age-related kinematic performance should be considered during fast head-neck rotation target task in individuals aged from 8 to 85 years old. PeerJ 7:e7095 https://doi.org/10.7717/peerj.7095