Abstract
Background
Microbiome/metagenomic data have specific characteristics, including varying total sequence reads, over-dispersion, and zero-inflation, which require tailored analytic tools. Many ...microbiome/metagenomic studies follow a longitudinal design to collect samples, which further complicates the analysis methods needed. A flexible and efficient R package is needed for analyzing processed multilevel or longitudinal microbiome/metagenomic data.
Results
NBZIMM is a freely available R package that provides functions for setting up and fitting negative binomial mixed models, zero-inflated negative binomial mixed models, and zero-inflated Gaussian mixed models. It also provides functions to summarize the results from fitted models, both numerically and graphically. The main functions are built on top of the commonly used R packages nlme and MASS, allowing us to incorporate the well-developed analytic procedures into the framework for analyzing over-dispersed and zero-inflated count or proportion data with multilevel structures (e.g., longitudinal studies). The statistical methods and their implementations in NBZIMM particularly address the data characteristics and the complex designs in microbiome/metagenomic studies. The package is freely available from the public GitHub repository
https://github.com/nyiuab/NBZIMM
.
Conclusion
The NBZIMM package provides useful tools for complex microbiome/metagenomics data analysis.
This study investigates whether the initiation time and intensification rate (INTRATE) of intensifying tropical cyclones (TCs) vary diurnally and how they are related to deep convection. TC ...intensifying events are identified and classified into slowly intensifying (SI) and rapidly intensifying (RI) events. RI events last ∼42 hr on average, much longer than SI events. More importantly, the onset of the TC intensification, especially RI, markedly peaks at 00–06 local time. However, the INTRATEs of both RI and SI events show very weak diurnal variability. The INTRATE continues to increase after RI initiation and slightly peaks in the late afternoon (at 90% significance level). Inner‐core convection of all intensifying events maximizes in the early morning, in phase with the peak initiation time. In short, our results suggest that the nocturnally enhanced inner‐core convection may play a role in triggering TC intensification (e.g., RI), but not maximizing the INTRATE.
Plain Language Summary
The outbreak of intense convection in the inner core of tropical cyclones (TCs) may promote the rapid intensification of TCs. It is well known that TC inner‐core convection varies diurnally. Recent studies found that the TC intensification rate exhibits a diurnal cycle that is in phase with the inner‐core deep convection. These studies further proposed that the nocturnally enhanced inner‐core convection may simultaneously promote the TC intensification rate. However, it is unknown whether and how the diurnal cycle of the intensification rate varies among different TC intensifying periods. Also, whether the initial time of the TC intensification exhibits an evident diurnal signal? Based on the analysis of 30‐year TC track data, this study found that TC intensification including the RI prefers to initiate in the early morning, well in phase with the inner‐core deep convection. In contrast, the intensification rate of RI TCs continues to increase after RI initiation therefore does not peak immediately with the deep convection. These results suggest that the inner‐core convective outbreak may be important in triggering the TC intensification especially RI, while the intensification rate is impacted or dominated by multiple factors that are not on the diurnal scale.
Key Points
The rapid intensification (RI) of tropical cyclone (TC) is more likely to initiate in the early morning and lasts ∼42 hr on average
TC intensification rates of RI events slightly peak in the late afternoon but with a marginal diurnal amplitude
Inner‐core deep convection likely plays a role in the RI initiation as they are diurnally in phase
In order to reduce the energy consumption of buildings, an air source heat pump assisted rooftop photovoltaic-thermal integration system is designed. The installation area of photovoltaic modules and ...collectors will not only affect the power side, but also affect the thermal side. Therefore, the basic architecture of the photovoltaic photothermal integration system is first established, and then the improved whale algorithm is used to optimize the photovoltaic photothermal integration system with the daily operating cost as the optimization goal. At the same time, the influence of the installation area of the photovoltaic photothermal module on the comprehensive performance of the system is analyzed, and the environmental and economic benefits of the photovoltaic photothermal system are analyzed. The results of the example show that the roof of the building has significant benefits in environmental protection and investment recovery period when the photovoltaic photothermal system with the optimal area ratio is installed on the roof of the building. The solar photovoltaic power generation system can reduce carbon dioxide emissions by 147.11 t within 25 years, and the solar collector system can save 170.5 thousand yuan in 1 year. It has achieved the purpose of saving energy, reducing carbon dioxide emissions and protecting the environment.
To develop predictive criteria for COVID-19-associated cytokine storm (CS), a severe hyperimmune response that results in organ damage in some patients infected with COVID-19. We hypothesised that ...criteria for inflammation and cell death would predict this type of CS.
We analysed 513 hospitalised patients who were positive for COVID-19 reverse transcriptase PCR and for ground-glass opacity by chest high-resolution CT. To achieve an early diagnosis, we analysed the laboratory results of the first 7 days of hospitalisation. We implemented logistic regression and principal component analysis to determine the predictive criteria. We used a 'genetic algorithm' to derive the cut-offs for each laboratory result. We validated the criteria with a second cohort of 258 patients.
We found that the criteria for macrophage activation syndrome, haemophagocytic lymphohistiocytosis and the HScore did not identify the COVID-19 cytokine storm (COVID-CS). We developed new predictive criteria, with sensitivity and specificity of 0.85 and 0.80, respectively, comprising three clusters of laboratory results that involve (1) inflammation, (2) cell death and tissue damage, and (3) prerenal electrolyte imbalance. The criteria identified patients with longer hospitalisation and increased mortality. These results highlight the relevance of hyperinflammation and tissue damage in the COVID-CS.
We propose new early predictive criteria to identify the CS occurring in patients with COVID-19. The criteria can be readily used in clinical practice to determine the need for an early therapeutic regimen, block the hyperimmune response and possibly decrease mortality.
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•Soy protein isolate/chitosan (SPI-CS) nanoparticles were obtained as stabilizers.•SPI-CS nanoparticles could stabilize Pickering emulsions at a low concentration.•Particle content ...and oil fraction affect properties of SPI-CS Pickering emulsions.•SPI-CS Pickering emulsions were stable at high ionic strength and temperature.
This work aimed to investigate the feasibility of fabricating food-grade Pickering emulsions stabilized by soy protein isolate-chitosan (SPI-CS) nanoparticles. The SPI-CS nanoparticles were characterized by scanning electron microscopy and particle size analyzer. Pickering emulsion stabilized by SPI-CS nanoparticles were characterized by confocal laser scanning microscopy and optical microscopy. The results showed that the average size of SPI-CS nanoparticles was 148.52 ± 1.95 nm. The droplet sizes of Pickering emulsions at different nanoparticle concentrations and oil fractions were 11.80 ± 2.20–43.68 ± 4.12 μm. SPI-CS nanoparticles stabilized Pickering emulsions at different nanoparticle concentrations and oil fractions had low creaming index, and these Pickering emulsions were stable at 4 °C for 20 days. These SPI-CS Pickering emulsions were stable at broad ionic strengths (0–1000 mM) and temperature (4–60 °C). These findings may provide new insight into the development of food-grade Pickering emulsions suitable for the formulation of functional foods.
•Deadenylation of mRNAs triggers bulk mRNA decay.•Uncapped mRNAs can be degraded cotranslationally in plants.•mRNA surveillance pathways sort out dysfunctional transcripts for degradation.•mRNA decay ...represses unnecessary RNA silencing and protects plant transcriptome.
In eukaryotes, degradation of messenger RNAs (mRNAs) is required for both mRNA quantity and quality control. Fine-tuning of the abundance of mRNAs that are to be translated can be achieved through a deadenylation-mediated RNA decay pathway involving progressive removal of poly(A) tails, decapping and exoribonuclease digestion. While the classical view assumes that mRNAs are degraded only after their exit from protein translation, recent studies have revealed mRNA decay can occur during translation in plants. Those mRNAs that have structural or functional defects can be filtered by translation-dependent RNA quality control pathways and rapidly degraded, so that translation fidelity is preserved. In addition, aberrant transcripts can also be efficiently eliminated through bidirectional RNA decay pathways. In the absence of those pathways, accumulation of those aberrant transcripts evokes the activation of RNA silencing, with detrimental consequences.
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•Multimode ultrasound extraction raised the polysaccharide (LMP) yield efficiently.•The highest yield of LMP was achieved with 20/35 alternation ultrasound treatment.•The composition ...of LMP extracted by ultrasonic was arabinose, galactose, glucose.•Purified LMP treated with ultrasound exerted remarkable immunoregulatory activity.
This study evaluates the effect of multimodal ultrasound on the extraction efficiency and immunoregulatory activity of polysaccharides from Lepidium meyenii Walp. (LMP). The separation and purification of maca polysaccharides were investigated by the DEAE-52 cellulose column, and the monosaccharide compositions were identified by HPGPC. Their immune activity was analyzed by the secretion of cytokines (TNF-α and IL-6) from RAW 264.7 macrophage. The results showed that the optimal extraction conditions were energy aggregation alternation dual-frequency ultrasound (EADU) with frequency combinations of 20/35, extraction time of 15 min, material/water ratio of 1:10 g/mL, ultrasonic power intensity of 150 W/L, intermittent time ratio of 4 s/3 s, and extraction temperature of 50 ℃. The extraction rates of purified polysaccharides (US3) increased by 44.90%. The LMP extracted by EADU contained arabinose, galactose, and glucose in the molar ratios of 2.9:2.72:5.05. In addition, US3 promoted the release of TNF-α and IL-6 from RAW 264.7 better than RS3 (purified polysaccharides extracted by hot water), which indicated that US3 exerted remarkable immune activity. It could be an excellent functional additive in food or medicine.
Peer-to-peer (P2P) technology has found much success in applications like file distributions and VoIP yet, its adoption in live video streaming remains as an elusive goal. Our recent success in ...Coolstreaming system brings promises in this direction; however, it also reveals that there exist many practical engineering problems in real live streaming systems over the Internet. Our focus in this paper is on a nonoptimal real working system, in which we illustrate a set of existing practical problems and how they could be handled. We believe this is essential in providing the basic understanding of P2P streaming systems. This paper uses a set of real traces and attempts to develop some theoretical basis to demonstrate that a random peer partnership selection with a hybrid pull-push scheme has the potentially to scale. Specifically, first, we describe the fundamental system design tradeoffs and key changes in the design of a Coolstreaming system including substreaming, buffer management, scheduling and the adopt of a hybrid pull-push mechanism over the original pull-based content delivery approach; second, we examine the overlay topology and its convergence; third, using a combination of real traces and analysis, we quantitatively provide the insights on how the buffering technique resolves the problems associated with dynamics and heterogeneity; fourth, we show how substream and path diversity can help to alleviate the impact from congestion and churns; fifth, we discuss the system scalability and limitations.
The Multiple Microgrid System (MMG) facilitates synergistic complementarity among various energy sources, reduces carbon emissions, and promotes the integration of renewable energy generation. In ...this context, we propose a two-stage robust cooperative scheduling model for MMGs based on non-cooperative game theory and a benefit allocation mechanism. In the first stage, considering electricity price fluctuations and uncertainties in wind and solar power outputs, a robust optimization approach is applied to establish an electric energy management model for MMGs. This model enables point-to-point energy sharing among microgrids. In the second stage, addressing the benefit allocation problem for shared electric energy, we introduce a Cost Reduction Ratio Distribution (CRRD) model based on non-cooperative game theory. The generalized Nash equilibrium is utilized to determine the benefit distribution for shared electric energy. Finally, through case studies, the proposed model is validated, ensuring fair returns for each microgrid. The results indicate that the proposed model optimizes the operational states of individual microgrids, reduces operational costs for each microgrid, and lowers the overall total operational costs of the MMG system. Additionally, an investigation is conducted into the impact of electricity price uncertainty coefficients and confidence levels of wind and solar uncertainties on the operational costs of microgrids.
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