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Generalized Additive Models (GAMs) are widely employed in ecological research, serving as a powerful tool for ecologists to explore complex nonlinear relationships between a response variable and predictors. Nevertheless, evaluating the relative importance of predictors with concurvity (analogous to collinearity) on response variables in GAMs remains a challenge. To address this challenge, we developed an R package named gam.hp. gam.hp calculates individual R2 values for predictors, based on the concept of ‘average shared variance’, a method previously introduced for multiple regression and canonical analyses. Through these individual R2s, which add up to the overall R2, researchers can evaluate the relative importance of each predictor within GAMs. We illustrate the utility of the gam.hp package by evaluating the relative importance of emission sources and meteorological factors in explaining ozone concentration variability in air quality data from London, UK. We believe that the gam.hp package will improve the interpretation of results obtained from GAMs.

The grain filling rate (GFR) plays a crucial role in determining grain yield. However, the regulatory and molecular mechanisms of the grain filling rate (GFR) in foxtail millet remains unclear. In this study, we found that the GFR of ′Changnong No.47′ (CN47) was significantly higher at 14 DAF (days after flowering) and 21 DAF in comparison to ‘Changsheng 13’ (CS13). Furthermore, CN47 also exhibited higher a thousand-grain weight and yield than CS13. Therefore, RNA-seq and UHPLC-MS/MS were used to conduct transcriptome and metabolome analyses during two stages of grain filling in both cultivars. Conjoint analysis of transcriptomics and metabolomics was adopted in order to analyze the biological processes and functional genes associated with GFR. The results identified a total of 765 differentially expressed genes (DEGs) and 246 differentially accumulated metabolites (DAMs) at the 14 DAF stage, while at the 21 DAF stage, a total of 908 DEGs and 268 DAMs were identified. The integrated analysis of co-mapped DAMs and DEGs revealed enriched pathways, including flavonoid biosynthesis, plant hormone signal transduction, tyrosine metabolism, ATP-binding cassette (ABC) transporters, and beta-Alanine metabolism, as well as stilbenoid, diarylheptanoid, and gingerol biosynthesis. In order to elucidate their potential functions in the context of GFR, we developed a gene–metabolite regulatory network for these metabolic pathways. Notably, we found that some genes associated with ABC transporters and the plant hormone signal transduction pathway were implicated in auxin transport and signal transduction, highlighting the crucial role of auxin during grain filling. These findings provide initial insights into the regulatory and molecular mechanisms underlying GFR in foxtail millet, as well as offering valuable genetic resources for further elucidation of GFR in future studies. The findings have also established a theoretical basis for improving the efficiency of yield breeding in foxtail millet.

Abstract Background Bacterial infection of adenoid is currently considered to be an important cause of adenoid hypertrophy (AH) in children. Although several bacteriology studies on adenoid diseases have been reported, the aerobic bacterial study regarding risk factors and antibiotic sensitivity of AH in Chinese children is lacking. This study aims to investigate the risk factors for aerobic bacterial colonization of AH in Chinese children and to elucidate aerobic bacterial profiles and antibiotic sensitivity. Methods Samples were collected from the adenoid core and surface tissue of 466 children undergoing adenoidectomy. Aerobic cultures and antibiotic sensitivity were observed. The risk factors for bacterial colonization of adenoid were analyzed statistically. Results A total of 143 children could be detected opportunistic pathogens in adenoid surface and/or core tissue, with a carriage rate of 30.7%. The presence of chronic rhinosinusitis, tonsillar hypertrophy and adenoidal size were the risk factors for aerobic bacterial colonization of adenoid in univariate analysis. Multivariate analysis showed that chronic rhinosinusitis and tonsil hypertrophy were significant variables associated with the aerobic bacterial colonization. The most frequently isolated aerobic bacteria were Haemophilus influenzae, followed by Staphylococcus aureus and Streptococcus pneumoniae. There was no statistically significant difference in bacterial species between the adenoid surface and core. The above common bacteria were more sensitive to cephalosporins and quinolones antibiotics, and significantly resistant to penicillin antibiotics and non-β-lactamase inhibitors. Conclusion Our results provide recent aerobic bacterial profiles for AH among Chinese children and confirm the risk factors and antibiotic sensitivity. This study contributes to understanding the role of different risk factors in the development of AH and will be helpful to the treatment of AH among Chinese children.

Over the past fifty years, the distribution patterns of C4 species, across large spatial scales, are largely ignored. Here, we endeavored to examine patterns in the taxonomic and phylogenetic diversity of species with C4 photosynthetic pathways across the broad spatial extent of China and relate those to climatic gradients. We built a database of all plants with the C4 photosynthetic pathway in China. We analyzed the geographic distributions, taxonomic diversity, phylogenetic diversity, and phylogenetic structure of all C4 species, as well as the three families with the most C4 species (Poaceae, Amaranthaceae and Cyperaceae), and compared their values along temperature and precipitation gradients at two scales—the level of the province and at the 100 x 100 km grid cell. We found 644 C4 plants (belonging to 23 families 165 genera) in China, with Poaceae (57%), Amaranthaceae (17%), Cyperaceae (13%) accounting for the majority of species. Standardized effect size values of phylogenetic distances were negative overall, indicating that C4 species showed a phylogenetic clustering pattern. Southern China had the highest species richness and the highest degree of phylogenetic clustering. C4 tended to be more phylogenetically over-dispersed in regions with colder and/or drier climates, but more clustered in warmer and/or wetter climates. Patterns within individual families were more nuanced. The distribution of C4 species and its phylogenetic structure across China was constrained by temperature and precipitation. C4 species showed a phylogenetic clustering pattern across China, while different families showed more nuanced responses to climate variation, suggesting a role for evolutionary history.

Functional connectivity (FC) between brain region has been widely studied and linked with cognition and behavior of an individual. FC is usually defined as the correlation or partial correlation of fMRI blood oxygen level-dependent (BOLD) signals between two brain regions. Although FC has been effective to understand brain organization, it cannot reveal the direction of interactions. Many directed acyclic graph (DAG) based methods have been applied to study the directed interactions but their performance was limited by the small sample size while high dimensionality of the available data. By enforcing group regularization and utilizing samples from both case and control groups, we propose a joint DAG model to estimate the directed FC. We first demonstrate that the proposed model is efficient and accurate through a series of simulation studies. We then apply it to the case-control study of schizophrenia (SZ) with data collected from the MIND Clinical Imaging Consortium (MCIC). We have successfully identified decreased functional integration, disrupted hub structures and characteristic edges (CtEs) in SZ patients. Those findings have been confirmed by previous studies with some identified to be potential markers for SZ patients. A comparison of the results between the directed FC and undirected FC showed substantial differences in the selected features. In addition, we used the identified features based on directed FC for the classification of SZ patients and achieved better accuracy than using undirected FC or raw features, demonstrating the advantage of using directed FC for brain network analysis.

Considering the metal-based nanocrystal (NC) hierarchical structure requirements in many real applications, starting from basic synthesis principles of electrostatic spinning technology, the formation of functionalized fibrous materials with inorganic metallic and semiconductor nanocrystalline materials by electrostatic spinning synthesis technology in recent years was reviewed. Several typical electrostatic spinning synthesis methods for nanocrystalline materials in polymers are presented. Finally, the specific applications and perspectives of such electrostatic spun nanofibers in the biomedical field are reviewed in terms of antimicrobial fibers, biosensing and so on.

Abstract Background Hepatocellular carcinoma (HCC) is the major pathological type of primary liver cancer, one of the leading causes of cancer death worldwide. In addition, the long-term survival rates of HCC still remain low. Therefore, we attempted to identify the potential key genes in the occurrence of HCC by comparing the expression profiles of very early HCC tissue samples with that of chronic cirrhotic tissue samples by integrating the bioinformatics analysis in this study. Methods Gene expression profiles of 19 very early HCC and 19 cirrhotic tissue samples were selected from GSE63898. Differentially expressed genes (DEGs) were also identified by using online tool GEO2R. Furthermore, the GO and KEGG enrichment analysis of the DGEs were conducted on DAVID datasets. Then a protein–protein interaction (PPI) network was constructed and the modules were analyzed based on STRING database and Cytoscape software. The hub genes were screened by applying the cytoHubba plugin and then analyzed with the Kaplan Meier plotter. Results A total of 118 DEGs were identified between very early HCC and cirrhotic tissue samples. These DGEs were strongly associated with several biological processes, such as negative regulation of growth and p53 signaling pathway. A PPI network was constructed and top eight hub genes, including CDKN3, CDK1, CCNB1, TOP2A, CCNA2, CCNB2, PRC1, and RRM2, were determined. High expressions of CDK1, CCNB1, TOP2A, CCNA2, PRC1, RRM2, CDKN3, and CCNB2 were associated with poorer overall survivals (OS) in HCC patients. Conclusion We had compared the expression profiles between the very early HCC and cirrhotic tissue samples by using bioinformatics analysis tools, which might help us better to understand the molecular mechanism of the initiation of HCC and even to find novel targets for HCC therapy.

Recently, functional network connectivity (FNC) has been extended from static to dynamic analysis to explore the time-varying functional organization of brain networks. Nowadays, a majority of dynamic FNC (dFNC) analysis frameworks identified recurring FNC patterns with linear correlations based on the amplitude of fMRI time series. However, the brain is a complex dynamical system and phase synchronization provides more informative measures. This paper proposes a novel framework for the prediction/classification of behaviors and cognitions based on the dFNCs derived from phase locking value. When applying to the analysis of fMRI data from Human Connectome Project (HCP), four dFNC states are identified for the study of sleep quality. State 1 exhibits most intense phase synchronization across the whole brain. States 2 and 3 have low and weak connections, respectively. State 4 exhibits strong phase synchronization in intra and inter-connections of somatomotor, visual and cognitive control networks. Through the two-sample t-test, we reveal that for the group with bad sleep quality, state 4 shows decreased phase synchronization within and between networks such as subcortical, auditory, somatomotor and visual, but increased phase synchronization within cognitive control network, and between this network and somatomotor/visual/default-mode/cerebellar networks. The networks with increased phase synchronization in state 4 behave oppositely in state 2. Group differences are absent in state 3, and weak in state 1. We establish a prediction model by linear regression of FNC against sleep quality, and adopt a support vector machine approach for the classification. We compare the performance between conventional FNC and PLV-based dFNC with cross-validation. Results show that the PLV-based dFNC significantly outperforms the conventional FNC in terms of both predictive power and classification accuracy. We also observe that combining static and dynamic features does not significantly improve the classification over using dFNC features alone. Overall, the proposed approach provides a novel means to assess dFNC, which can be used as brain fingerprints to facilitate prediction and classification.

Invasive species are a subset of naturalized species, and naturalized species are a subset of alien species. Determining the relationship among these three assemblages would be helpful in predicting and preventing biological invasion. Here, we reviewed the families, lifeforms, origins, introduction pathways and phylogenetic diversity of alien, naturalized and invasive vascular plants in China. The results show that species in the Asteraceae, Fabaceae and Poaceae families had a high dominance among alien, naturalized and invasive species. Moreover, almost all alien species in the Amaranthaceae, Solanaceae, Convolvulaceae and Euphorbiaceae families became naturalized species, and about 26.7% of the naturalized species became invasive species. Perennial herbs comprised a higher proportion of alien species than did annual herbs, though annual herbs were more suited to becoming invasive than perennial herbs. A considerable proportion (57.8%) of invasive species were introduced from America. More than half (56.5%) of alien species were introduced for their ornamental value, and half of these have become naturalized in China. Moreover, about half (55.2%) of all invasive species were introduced for their economic value (including ornamental, foraging and medicinal purposes). Invasive species were phylogenetically clustered and phylogenetically distant from alien and naturalized species, which indicates that phylogenetic differences could be helpful in becoming invasive. There is no doubt that human activity plays a significant role in biological invasion. This study suggests that when introducing alien species to a region, decision-makers should certainly consider the species’ phylogeny, beyond just its fundamental characteristics.

Accelerating and severe wetland loss has made wetland restoration increasingly important. Current wetland restorations do not take into consideration the ecological adaptability of wetland plants at large scales, which likely affects their long-term restoration success. We explored the ecological adaptability, including plant life forms and phylogenetic diversity, of plants across 28 wetlands in China. We found that perennial herbs were more common than annual herbs, with the proportion of perennial herbs accounting for 40–50%, 45–65%, 45–70%, 50–60%, and 60–80% of species in coastal wetlands, human-made wetlands, lake wetlands, river wetlands, and marsh wetlands, respectively. A ranking of phylogenetic diversity indices (PDIs) showed an order of marsh < river < coastal < lake < human-made, meaning that human-made wetlands had the highest phylogenetic diversity and marsh wetlands had the lowest phylogenetic diversity. The nearest taxon index (NTI) was positive in 23 out of 28 wetlands, indicating that species were phylogenetically clustered in wetland habitats. Dominant species tended to be distantly related to non-dominant species, as were alien invasive species and native species. Our study indicated that annual herbs and perennial herbs were found in different proportions in different types of wetlands and that species were phylogenetically clustered in wetland habitats. To improve wetland restoration, we suggest screening for native annual herbs and perennial herbs in proportions that occur naturally and the consideration of the phylogenetic similarity to dominant native species.

Objectives This study aimed to examine a simple, effective, time-saving, and low-cost protein microarray method for detecting serum alpha-fetoprotein (AFP) and AFP-L3 levels. Methods Serum samples from patients with hepatocellular carcinoma (HCC) (n = 33) and control subjects (n = 39) were collected and evaluated for the presence of AFP using a novel protein microarray. Glycoprotein (including AFP-L3) was enriched from crude samples by a Hotgen Biotech glycosyl capture spin column and then detected by protein microarray. An electrochemiluminescence immunoassay (ECLIA) was used to validate the measured values. Results Neither AFP levels lower than 20 ng/mL in the HCC group nor AFP levels higher than 20 ng/mL in the control group were found when tested by the ECLIA and protein microarray. The kappa test showed good consistency in the diagnostic performance of measuring serum AFP levels and the percentage of AFP-L3 in total AFP by the ECLIA and protein microarray. Protein microarray had advantages of smaller sample size required, low cost, and convenience compared with the ECLIA. Conclusion The protein microarray assay that was developed in the present study shows potential as an economic and convenient technique for detecting AFP and AFP-L3 levels in serum samples from patients with HCC.

Alzheimer's disease (AD) is a devastating neurodegenerative disease that affects millions of seniors in the United States. Resting-state functional magnetic resonance imaging (rs-fMRI) is widely used to study neurophysiology in AD and its prodromal condition, mild cognitive impairment (MCI). The intrinsic neural timescale (INT), which can be estimated through the magnitude of the autocorrelation of neural signals from rs-fMRI, is thought to quantify the duration that neural information is stored in a local circuit. Such heterogeneity of the timescales forms a basis of the brain functional hierarchy and captures an aspect of circuit dynamics relevant to excitation/inhibition balance, which is broadly relevant for cognitive functions. Given that, we applied rs-fMRI to test whether distinct changes of INT at different hierarchies are present in people with MCI, those progressing to AD (called Converter), and AD patients of both sexes. Linear mixed-effect model was implemented to detect altered hierarchical gradients across populations followed by pairwise comparisons to identify regional differences. High similarities between AD and Converter were observed. Specifically, the inferior temporal, caudate, and pallidum areas exhibit significant alterations in both AD and Converter. Distinct INT-related pathological changes in MCI and AD were found. For AD/Converter, neural information is stored for a longer time in lower hierarchical areas, while higher levels of hierarchy seem to be preferentially impaired in MCI leading to a less pronounced hierarchical gradient. These results inform that the INT holds great potential as an additional measure for AD prediction, even a stable biomarker for clinical diagnosis. [ABSTRACT FROM AUTHOR]

Over the past fifty years, the distribution patterns of C4 species, across large spatial scales, are largely ignored. Here, we endeavored to examine patterns in the taxonomic and phylogenetic diversity of species with C4 photosynthetic pathways across the broad spatial extent of China and relate those to climatic gradients. We built a database of all plants with the C4 photosynthetic pathway in China. We analyzed the geographic distributions, taxonomic diversity, phylogenetic diversity, and phylogenetic structure of all C4 species, as well as the three families with the most C4 species (Poaceae, Amaranthaceae and Cyperaceae), and compared their values along temperature and precipitation gradients at two scales--the level of the province and at the 100 x 100 km grid cell. We found 644 C4 plants (belonging to 23 families 165 genera) in China, with Poaceae (57%), Amaranthaceae (17%), Cyperaceae (13%) accounting for the majority of species. Standardized effect size values of phylogenetic distances were negative overall, indicating that C4 species showed a phylogenetic clustering pattern. Southern China had the highest species richness and the highest degree of phylogenetic clustering. C4 tended to be more phylogenetically over-dispersed in regions with colder and/or drier climates, but more clustered in warmer and/or wetter climates. Patterns within individual families were more nuanced. The distribution of C4 species and its phylogenetic structure across China was constrained by temperature and precipitation. C4 species showed a phylogenetic clustering pattern across China, while different families showed more nuanced responses to climate variation, suggesting a role for evolutionary history. [ABSTRACT FROM AUTHOR]