An issue for class‐imbalanced learning is what assessment metric should be employed. So far, precision‐recall curve (PRC) as a metric is rarely used in practice as compared with its alternative of ...receiver operating characteristic (ROC). This study investigates the performance of PRC as the evaluating criterion to address the class‐imbalanced data and focuses on the comparison of PRC with ROC. The advantages of PRC over ROC on assessing class‐imbalanced data are also investigated and tested on our proposed algorithm by tuning the whole model parameters in simulation studies and real data examples. The result shows that PRC is competitive with ROC as performance measurement for handling class‐imbalanced data in tuning the model parameters. PRC can be considered as an alternative but effective assessment for preprocessing (such as variable selection) skewed data and building a classifier in class‐imbalanced learning.
Summary
The flagellated eukaryote Trypanosoma brucei alternates between the insect vector and the mammalian host and proliferates through an unusual mode of cell division. Cell division requires ...flagellum motility‐generated forces, but flagellum motility exerts distinct effects between different life cycle forms. Motility is required for the final cell abscission of the procyclic form in the insect vector, but is necessary for the initiation of cell division of the bloodstream form in the mammalian host. The underlying mechanisms remain elusive. Here we carried out functional analyses of a flagellar axonemal inner‐arm dynein complex in the bloodstream form and investigated its mechanistic role in cytokinesis initiation. We showed that the axonemal inner‐arm dynein heavy chain TbIAD5‐1 and TbCentrin3 form a complex, localize to the flagellum, and are required for viability in the bloodstream form. We further demonstrated the interdependence between TbIAD5‐1 and TbCentrin3 for maintenance of protein stability. Finally, we showed that depletion of TbIAD5‐1 and TbCentrin3 arrested cytokinesis initiation and disrupted the localization of multiple cytokinesis initiation regulators. These findings identified the essential role of an axonemal inner‐arm dynein complex in cell division, and provided molecular insights into the flagellum motility‐mediated cytokinesis initiation in the bloodstream form of T. brucei.
Trypanosoma brucei, a flagellated parasite causing human sleeping sickness in Africa, divides through binary cell fission, which depends on flagellar motility in the bloodstream stage, but the underlying mechanism is unclear. Here we show that depletion of a flagellar axonemal inner‐arm dynein complex in the bloodstream form of T. brucei disrupts the localization of multiple cytokinesis initiation regulators, which provides some molecular insights into the flagellar motility‐mediated cytokinesis initiation in T. brucei.
Imbalanced domain prediction analysis is currently one of the hot research topics. Many real‐world data mining analyses involve using imbalanced data to obtain predictive models. In the context of ...imbalance, research on classification problems has been extensive, but research on regression problems is negligible. Rare values rarely occur in imbalanced regression problems, but the focus is on accurately predicting the continuous target variables of rare instances. One of the challenges in imbalanced regression is finding a suitable strategy to rebalance the original dataset in order to improve the predictive performance of the model in rare instances. In this study, two algorithms are proposed: sigma nearest over‐sampling based on convex combination for regression (SNOCCR) and affine combination‐based over‐sampling (ACOS). ACOS rebalances the original dataset by generating new instances through the affine combinations of the original examples. The region where the new instances are generated can be adjusted based on the distribution of the data, ensuring that the generated cases better mimic the distribution of the original examples. The comparison among ACOS, SNOCCR, and other preprocessing methods was conducted on 15 datasets to validate the predictive performance of models trained on rebalanced datasets for rare instances. The experimental results indicate that ACOS outperforms other existing methods.
In this study, two over‐sampling algorithms are proposed: sigma nearest over‐sampling based on convex combination for regression (SNOCCR) and affine combination‐based over‐sampling (ACOS) in order to improve the predictive performance of the model in imbalanced regression. The experimental results indicate that ACOS outperforms other existing methods.
A contribution of DNA methylation to defense against invading nucleic acids and maintenance of genome integrity is uncontested; however, our understanding of the extent of involvement of this ...epigenetic mark in genome-wide gene regulation and plant developmental control is incomplete. Here, we knock out all five known DNA methyltransferases in Arabidopsis, generating DNA methylation-free plants. This quintuple mutant exhibits a suite of developmental defects, unequivocally demonstrating that DNA methylation is essential for multiple aspects of plant development. We show that CG methylation and non-CG methylation are required for a plethora of biological processes, including pavement cell shape, endoreduplication, cell death, flowering, trichome morphology, vasculature and meristem development, and root cell fate determination. Moreover, we find that DNA methylation has a strong dose-dependent effect on gene expression and repression of transposable elements. Taken together, our results demonstrate that DNA methylation is dispensable for Arabidopsis survival but essential for the proper regulation of multiple biological processes.
Management strategies for the safe disposal of contaminated dredged marine sediment constitute a global-scale environmental issue. The stabilization/solidification method was investigated as a ...sustainable approach to the recycling of the sediment as a construction material. A systematic study of the factors affecting the mechanical performance and contaminant release was performed. The physico-chemical variables selected to assess the potential re-use of the sediment treated with Ordinary Portland cement (OPC) and Ground Granulated Blast Furnace Slag (GGBS) in an aquatic environment were: curing duration (7, 28, 56 and 98 days), curing temperature (5, 20 and 40 °C) and ambient (leachate) pH (1, 4, 7 and 10). Unconfined compressive strength (UCS) tests were conducted and extended-duration tank leaching tests were used to characterize the long-term leaching of Al, Cr, Mn, Fe, Ni, Cu, Zn, As, Cd, Ba, Pb. The results showed that S/S methods provide excellent immobilization of metals in marine sediment at a pH range of 4 to 10. Immobilization efficiencies of >99.9% for Mn, Fe, Zn, As, Ba, Pb and >97.8% for Al, Cu and Zn are reported over 100 days. GGBS replacement is an effective way to further improve sediment properties by enhancing strength, mitigating sediment alkalization and offering a better immobilization capacity for Fe, Ni and Zn. The release of metals (Al, Mn, Cu, As, Ba and Pb) was strongly associated with a coupling effect of the physico-chemical factors, with metal-specific responses to curing temperature, curing duration and pH. Mn mobility showed a dramatic sensitivity to ambient pH while Ba was less pH-dependent. Al release is related to strength and leached out by dissolution in all situations considered. Considering that dredged marine sediments may contain multiple metal contaminants which exhibit individual responses to remediation, treatment with GGBS may be considered a potentially suitable management option.
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•Several factors influencing mechanical and leaching behavior of S/S sediments were studied.•GGBS replacement offers better fixation than OPC for Fe, Ni and Zn under any conditions.•Al release is related to strength and leached out by the way of dissolution.•Optimal temperature for GGBS mixes is effective for immobilizing Al, As, Ba, Pb.
Summary Streptococcus suis is a major porcine pathogen worldwide, and can be transmitted to human beings by close contact with sick or carrier pigs. S suis causes meningitis, septicaemia, ...endocarditis, arthritis, and septic shock in both pigs and human beings, and mortality is high. Human infection with S suis occurs mainly among certain risk groups that have frequent exposure to pigs or pork. Outbreaks of human S suis infection are uncommon, although several outbreaks have occurred in China in recent years. In July, 2005, the largest outbreak of human S suis infection occurred in Sichuan province, China, where 204 people were infected and 38 of them died. There have been 409 cases of human S suis infection worldwide, most of which have occurred in China, Thailand, and the Netherlands, and these infections have led to 73 deaths. This review provides background information on the biology and molecular characteristics of this Gram-positive bacterium, and describes the clinical signs, pathology, epidemiology, diagnosis, and treatment of human infection with S suis.
The aim of this study was to investigate and quantify the association between oxygen concentration and life expectancy. The data from 34 provinces and 39 municipalities were included in all analyses. ...Bayesian regression modeling with spatial-specific random effects was used to quantify the impact of oxygen concentration (measured as partial pressure of oxygen) on life expectancy, adjusting for other potential confounding factors. We used hierarchical cluster analysis to group the provinces according to disease burden and analyzed the oxygen levels and the characteristics of causes of death between the clusters. The Bayesian regression analysis showed that the life expectancy at the provincial level increased by 0.15 (95% CI: 0.10-0.19) years, while at the municipal level, it increased by 0.17 (95% CI: 0.12-0.22) years, with each additional unit (mmHg) of oxygen concentration, after controlling for potential confounding factors. Three clusters were identified in the hierarchical cluster analysis, which were characterized by different oxygen concentrations, and the years of life lost from causes potentially related to hypoxia were statistically significantly different between the clusters. A positive correlation was found between oxygen concentration and life expectancy in China. The differences in causes of death and oxygen levels in the provincial clusters suggested that oxygen concentration may be an important factor in life expectancy when mediated by diseases that are potentially related to hypoxia.
Feature selection and rebalancing can be seen as two preprocessing ways in class‐imbalanced learning. Recently, there have been many research achievements and applications on LASSO‐type feature ...selection, whereas most of them are not directly designed for addressing class‐imbalanced data. In this study, we proposed a LASSO‐based stable feature selection algorithm for class‐imbalanced data analysis, and false‐positive selection (FPS) under balanced and imbalanced situations was calculated via selection frequency of each predictor in doing stable selection. The results on simulation studies and real data examples show that class imbalance contributes to avoid overselection caused by LASSO when the data are highly correlated and a lower FPS can be obtained with class‐imbalanced data than balanced one in most of cases in the same settings. A statistical explanation was given for this phenomenon. In addition, it does not need to rebalance the class‐imbalanced data for performing such LASSO‐based feature selection with a stable strategy, and to some degree, intentionally disequilibrating the balanced data could be an alternative strategy to weaken overselection and to perform biomarker identification for finding a few of most important biomarkers.
A LASSO‐based stable feature selection algorithm was proposed for imbalanced data. It is not necessary to rebalance the imbalanced data with such stable feature selection strategy. Class imbalance even contributes to avoid overselection caused by LASSO when data are strongly correlated.
Artemisinin and its derivatives, in combination with partner drugs, are currently the most effective treatments for malaria parasite infection. Even though artemisinin has been widely used for ...decades, its mechanism of action had remained controversial until recently. Artemisinin combination therapies (ACTs) have recently been found to be losing efficacy in Southeast Asia. This ‘artemisinin resistance’, defined by a delayed parasite clearance time, has been associated with several genetic mutations. As with any other drug resistance phenotype, resistance can best be understood based on its mechanism of action. Recently, it was demonstrated that artemisinin attacks multiple parasitic targets, suggesting that mutations in drug targets are unlikely to cause high-level artemisinin resistance. These findings will help us to better understand the mechanisms of artemisinin resistance and suggest protocol modifications that may improve the efficacy of ACTs.
Unlike conventional classification paradigms, survival analysis confronts the intricacies engendered by partially observed data, often stemming from censoring. Within the realm of clinical inquiries, ...patient records manifest in distinct categories: those that remain uncensored, thereby divulging precise event timings, and those that exist as right-censored, withholding event timings beyond the study’s temporal scope. Careful consideration of censoring and time-to-event analysis principles is warranted.
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