DANCE: a deep learning library and benchmark platform for single-cell analysis.

DANCE is the first standard, generic, and extensible benchmark platform for accessing and evaluating computational methods across the spectrum of benchmark datasets for numerous single-cell analysis tasks. Currently, DANCE supports 3 modules and 8 popular tasks with 32 state-of-art methods on 21 benchmark datasets. People can easily reproduce the results of supported algorithms across major benchmark datasets via minimal efforts, such as using only one command line. In addition, DANCE provides an ecosystem of deep learning architectures and tools for researchers to facilitate their own model development. DANCE is an open-source Python package that welcomes all kinds of contributions.

Racial and ethnic and socioeconomic disparities in childhood cancer incidence trends in the United States, 2000-2019.

BACKGROUND: Population-based surveillance of pediatric cancer incidence trends is critical to determine high-risk populations, drive hypothesis generation, and uncover etiologic heterogeneity. We provide a comprehensive update to the current understanding of pediatric cancer incidence trends by sex, race and ethnicity, and socioeconomic status (SES). METHODS: The Surveillance, Epidemiology, and End Results 22 data (2000-2019) was used to summarize age-adjusted incidence rates for children and adolescents aged 0-19 years at diagnosis. The annual percentage change (APC) and 95% confidence interval (CI) were estimated to evaluate incidence trends by sex, race and ethnicity, and SES overall and for cancer subtypes. Tests of statistical significance were 2-sided. RESULTS: Substantial variation was observed overall and for several histologic types in race and ethnicity- and SES-specific rates. Overall, we observed a statistically significant increase in incidence rates (APC = 0.8%, 95% CI = 0.6% to 1.1%). All race and ethnic groups saw an increase in incidence rates, with the largest occurring among non-Hispanic American Indian and Alaska Native children and adolescents (APC = 1.7%, 95% CI = 0.5% to 2.8%) and the smallest increase occurring among non-Hispanic White children and adolescents (APC = 0.7%, 95% CI = 0.5% to 1.0%). The lowest SES quintiles saw statistically significant increasing trends, while the highest quintile remained relatively stable (quintile 1 [Q1] APC = 1.6%, 95% CI = 0.6% to 2.6%; quintile 5 [Q5] APC = 0.3%, 95% CI = -0.1% to 0.7%). CONCLUSIONS: Childhood cancer incidence is increasing overall and among every race and ethnic group. Variation by race and ethnicity and SES may enable hypothesis generation on drivers of disparities observed.

Effects of Typical Solvents on the Structural Integrity and Properties of Activated Kaolinite by Wet Ball Milling.

The influence of organic solvents on the structural integrity and properties of activated kaolinite were compared and analyzed via characterization techniques and molecular dynamics (MD) simulation. The results revealed that the organic intercalators can be easily inserted into the interlayer spaces of activated kaolinite within a short time of the wet ball milling. The DMSO intercalated kaolinites maintained structural integrity due to the high intercalation rate and the excellent buffering effect against the crushing force of milling during the delamination/exfoliation process. The delaminated layers of the DMSO-kaolinite complex exhibited a high specific surface area of 99.12 m2/g and a low average thickness of 35.21 nm. The calculated elastic properties of the organo-kaolinite complex manifested the intercalation of DMSO into a kaolinite interlayer, which could improve the compressibility and structural integrity of kaolinite nanosheets. The DMSO-kaolinite complex was easier to peel off when compared to the other organic intercalators due to its more intercalated molecules.

OXPHOS promotes apoptotic resistance and cellular persistence in TH17 cells in the periphery and tumor microenvironment.

T cell proliferation and cytokine production are bioenergetically and biosynthetically costly. The inability to meet these metabolic demands results in altered differentiation, accompanied by impaired effector function, and attrition of the immune response. Interleukin-17-producing CD4 T cells (TH17s) are mediators of host defense, autoimmunity, and antitumor immunity in the setting of adoptive T cell therapy. TH17s are long-lived cells that require mitochondrial oxidative phosphorylation (OXPHOS) for effector function in vivo. Considering that TH17s polarized under standardized culture conditions are predominately glycolytic, little is known about how OXPHOS regulates TH17 processes, such as their ability to persist and thus contribute to protracted immune responses. Here, we modified standardized culture medium and identified a culture system that reliably induces OXPHOS dependence in TH17s. We found that TH17s cultured under OXPHOS conditions metabolically resembled their in vivo counterparts, whereas glycolytic cultures were dissimilar. OXPHOS TH17s exhibited increased mitochondrial fitness, glutamine anaplerosis, and an antiapoptotic phenotype marked by high BCL-XL and low BIM. Limited mitophagy, mediated by mitochondrial fusion regulator OPA-1, was critical to apoptotic resistance in OXPHOS TH17s. By contrast, glycolytic TH17s exhibited more mitophagy and an imbalance in BCL-XL to BIM, thereby priming them for apoptosis. In addition, through adoptive transfer experiments, we demonstrated that OXPHOS protected TH17s from apoptosis while enhancing their persistence in the periphery and tumor microenvironment in a murine model of melanoma. Together, our work demonstrates how metabolism regulates TH17 cell fate and highlights the potential for therapies that target OXPHOS in TH17-driven diseases.

Stacked survival models for residual lifetime data.

When modelling the survival distribution of a disease for which the symptomatic progression of the associated condition is insidious, it is not always clear how to measure the failure/censoring times from some true date of disease onset. In a prevalent cohort study with follow-up, one approach for removing any potential influence from the uncertainty in the measurement of the true onset dates is through the utilization of only the residual lifetimes. As the residual lifetimes are measured from a well-defined screening date (prevalence day) to failure/censoring, these observed time durations are essentially error free. Using residual lifetime data, the nonparametric maximum likelihood estimator (NPMLE) may be used to estimate the underlying survival function. However, the resulting estimator can yield exceptionally wide confidence intervals. Alternatively, while parametric maximum likelihood estimation can yield narrower confidence intervals, it may not be robust to model misspecification. Using only right-censored residual lifetime data, we propose a stacking procedure to overcome the non-robustness of model misspecification; our proposed estimator comprises a linear combination of individual nonparametric/parametric survival function estimators, with optimal stacking weights obtained by minimizing a Brier Score loss function.

Erratum: Li, Z.; Zhang, W.; Wang, R.; Chen, F.; Jia, X.; Cong, P. Effects of Reactive MgO on the Reaction Process of Geopolymer. Materials 2019, 12, 526.

Author Contributions: Conceptualization, Z [...].

Effects of Reactive MgO on the Reaction Process of Geopolymer.

In order to compensate for the shrinkage of geopolymer pastes uniformly, reactive MgO powders are evenly dispersed in the geopolymer. The deformation performance, mechanical properties, microstructure and components of geopolymer pastes with reactive MgO are characterized. The effects of the content and the activity of MgO are discussed. The results indicate that the chemical shrinkage, autogenous shrinkage and drying shrinkage decrease with the addition of reactive MgO. MgO reacted with water, and fine Mg(OH)2 crystals forms as a geopolymer paste. Mg(OH)2 produces uniform expansion, which refines the pore size of pastes and the compressive strength increases. The shrinkage of the geopolymer pastes is thus effectively compensated.

Effect of the MgO/Silica Fume Ratio on the Reaction Process of the MgO⁻SiO2⁻H2O System.

In order to clarify the effect of the MgO⁻silica fume (SF) ratio on the reaction process of the MgO⁻SiO2⁻H2O system, the reaction products and degree of reaction were characterized. Furthermore, the parameters of the reaction thermodynamics were calculated and the reaction kinetics were deduced. The results indicate that a large amount of Mg(OH)2 and small quantities of magnesium silicate hydrate (M⁻S⁻H) gels were generated upon dissolution of MgO. However, the M⁻S⁻H gels were continuously generated until the SF or Mg(OH)2 was consumed completely. For a MgO dosage less than 50% of the total MgO⁻SiO2⁻H2O system, the main product was M⁻S⁻H gel, while for a MgO dosage greater than 50%, the main product was Mg(OH)2. The results indicate that M⁻S⁻H gels have greater stability than Mg(OH)2, and the final reaction product was prone to be M⁻S⁻H gels. Based on the experimental values, an equation is proposed for the reaction kinetics of MgO.