A statistical model for describing and simulating microbial community profiles.

Many methods have been developed for statistical analysis of microbial community profiles, but due to the complex nature of typical microbiome measurements (e.g. sparsity, zero-inflation, non-independence, and compositionality) and of the associated underlying biology, it is difficult to compare or evaluate such methods within a single systematic framework. To address this challenge, we developed SparseDOSSA (Sparse Data Observations for the Simulation of Synthetic Abundances): a statistical model of microbial ecological population structure, which can be used to parameterize real-world microbial community profiles and to simulate new, realistic profiles of known structure for methods evaluation. Specifically, SparseDOSSA's model captures marginal microbial feature abundances as a zero-inflated log-normal distribution, with additional model components for absolute cell counts and the sequence read generation process, microbe-microbe, and microbe-environment interactions. Together, these allow fully known covariance structure between synthetic features (i.e. "taxa") or between features and "phenotypes" to be simulated for method benchmarking. Here, we demonstrate SparseDOSSA's performance for 1) accurately modeling human-associated microbial population profiles; 2) generating synthetic communities with controlled population and ecological structures; 3) spiking-in true positive synthetic associations to benchmark analysis methods; and 4) recapitulating an end-to-end mouse microbiome feeding experiment. Together, these represent the most common analysis types in assessment of real microbial community environmental and epidemiological statistics, thus demonstrating SparseDOSSA's utility as a general-purpose aid for modeling communities and evaluating quantitative methods. An open-source implementation is available at http://huttenhower.sph.harvard.edu/sparsedossa2.

Multivariable association discovery in population-scale meta-omics studies.

It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata to microbial community measurements, due in part to their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and often in the form of count or compositional measurements. Here we introduce an optimized combination of novel and established methodology to assess multivariable association of microbial community features with complex metadata in population-scale observational studies. Our approach, MaAsLin 2 (Microbiome Multivariable Associations with Linear Models), uses generalized linear and mixed models to accommodate a wide variety of modern epidemiological studies, including cross-sectional and longitudinal designs, as well as a variety of data types (e.g., counts and relative abundances) with or without covariates and repeated measurements. To construct this method, we conducted a large-scale evaluation of a broad range of scenarios under which straightforward identification of meta-omics associations can be challenging. These simulation studies reveal that MaAsLin 2's linear model preserves statistical power in the presence of repeated measures and multiple covariates, while accounting for the nuances of meta-omics features and controlling false discovery. We also applied MaAsLin 2 to a microbial multi-omics dataset from the Integrative Human Microbiome (HMP2) project which, in addition to reproducing established results, revealed a unique, integrated landscape of inflammatory bowel diseases (IBD) across multiple time points and omics profiles.

Impacts of sanitation upgrading to the decrease of fecal coliforms entering into the environment in China.

Identifying the sanitation efficacy of reducing fecal contaminations in the environment is important for evaluating health risks of the public and developing future management strategies to improve sanitation conditions. In this study, we estimated the fecal coliforms (FC) entering into the environment in 31 provinces in China under three sanitation scenarios. Our calculation results indicated that, the current FC release is disparate among regions, and the human releases in the rural regions were dominant, accounting for over 90% of the total human releases. Compared with the human release, the FC release from the livestock was of similar magnitude, but has a quite different spatial distribution. In China Women's Development Program, the Chinese government set the target to make over 85% of the population in the rural access to the toilets in 2020. If the target set by the Chinese government is achieved, a decrease of 34% (12-54%) in the FC releases would be anticipated. In the future, the improvement in sanitation and accesses to the safe drinking water in the less developed regions, such as Tibet, Qinghai, and Ningxia, should be considered as a priority.

Phosphorylated silica nanotubes: preparation and characterization.

Recently, the strategy of doping inorganic particles into polymer membranes to modify them has been studied intensively. However, these inorganic particles have a disadvantage without being in good compatibility with the polymers. To enhance the compatibility between inorganic particles and polymers, phosphorylated silica nanotubes (PSNTs) with specific high ratios of length to diameter are prepared. Silica nanotubes (SNTs) are prepared through the hydrolysis of tetraethyl orthosilicate in a mixture of aqueous ammonia and dl-tartaric acid, then PSNTs are obtained by silylation and phosphorylation modifications. The optimum synthesis conditions of PSNTs are explored; in addition, the as-prepared PSNTs are characterized by Fourier transform infrared, transmission electron microscope, BET, x-ray photoelectron spectroscopy analysis and thermogravimetric analysis. The results indicate that the ratio of length to diameter of the PSNTs is approximately 20, the thickness of the tube wall is 20 nm, the specific surface area of the PSNTs is 460.2 m(2) g(-1), the inner diameter of the PSNTs is 76 nm, many mesopores are distributed in the tube walls of the PSNTs, and the PSNTs have numerous hydroxyl active sites along their length direction. Therefore, PSNTs are desirable as suitable fillers of polymer membranes.

Impact of dissolved organic matter and environmental factors on methylmercury concentrations across aquatic ecosystems inferred from a global dataset.

Mercury (Hg) input into ecosystems is estimated to have increased by twofold to fivefold since the industrial revolution. In aquatic ecosystems, methylmercury (MeHg) receives the most attentions of all the Hg species due to its neurotoxicity and strong bioaccumulation capacity in food chain. Dissolved organic matter (DOM) is crucial in impacting aquatic Hg transformation. However, only few spatially constrained studies have attempted to quantify the relative importance of DOM and other factors (e.g., Hg availability, temperature, pH, and land-use type) on MeHg concentration. In this study, we collected data of 585 water samples at 373 sites globally, including lakes, rivers, estuaries, and wetlands, and characterized the global pattern of MeHg distribution and environmental drivers of aquatic MeHg concentration. Our results showed that MeHg concentrations ranged from detection limits to 11 (geometric mean 0.11 and average 0.29) ng/L, and the highest MeHg concentration and Hg methylation potential were observed in wetlands. A positive relationship was observed between MeHg fraction in the total mercury (THg) and DOM for all the aquatic ecosystems. Using the structural equation modeling, we found that Hg availability was a dominant factor in impacting water MeHg concentration followed by DOM. According to 129 samples of specific DOM source information, we found that the percentage of THg as MeHg (%MeHg) in water dominated by the autochthonous DOM was higher than that dominated by the allochthonous DOM. Our results could advance understanding of aquatic Hg cycling and their environmental drivers, which are fundamental for predicting and mitigating MeHg productions and its potential health risks for humans.

[PAHs Pollution Characteristics and Source Analysis of Typical Lake and Reservoir Sediments in Jin-Ji-Liao Area].

In this research, 29 surface sediments samples of three typical lake reservoirs (in Yuqiao Reservoir, Hengshui Lake, and Dahuofang Reservoir) in the Jin-Ji-Liao area were collected and investigated, and the contents of 16 polycyclic aromatic hydrocarbons were detected using GC-MS. The results show that the Sigma PAHs (ng·g-1) in the sediments were 337.3-1604.1 (mean value 820.0), 461.1-1497.5 (mean value 932.3), and 102.3-2240.5 (mean value 564.9), respectively. Compared with other domestic rivers and lakes, the pollution levels of the PAHs in the three typical lakes were all at a medium level. The three lakes and reservoirs had consistency in the ratio of the number of rings, which is primarily high. PAHs source analyses were carried out by the characteristic ratio and primary component analysis method, and the results show that three lakes reservoirs pollution were caused mostly by combustion sources (including petroleum, coal, and biomass combustion), with a few petroleum sources. Additionally, the pollution contribution ratio of incomplete combustion of gasoline and diesel oil was 51.4%, and the pollution contribution ratio of combustion of coal and firewood were 22.3%. The risk evaluation results indicate that PAHs in the surface sediments of Yuqiao Reservoir, Hengshui Lake, and Dahuofang Reservoir are generally at a medium and low level, but the monitoring of three types of substances, Flu, InP, and DahA, should be strengthened, and corresponding emergency measures should be taken.

Impacts of water residence time on nitrogen budget of lakes and reservoirs.

As an important factor related to the self-purification capacity (e.g. denitrification, burial rate, and downstream output) in aquatic systems, water residence time (WRT) has great impacts on the nitrogen (N) dynamics and its removal process in lakes and reservoirs. In this study, we have analysed the impacts of WRT on the change rates of total nitrogen (TN) concentrations in 50 waterbodies (including 33 lakes and 17 reservoirs) in China, with different change trends (e.g. increasing trends and decreasing trends) and TN concentrations during 2012-2016. Based on the annual ecosystem-scale N mass balance, TN input and output flux in the waterbodies are estimated. The results showed that the decreases of TN concentrations usually occur in the waterbodies with the relatively high TN concentrations in 2012, and WRT has significant impacts on the TN change rates in the waterbodies. Longer WRT could slow down the TN increasing rates in the waterbodies acting as N sinks, but could accelerate the removal from the waterbodies acting as N sources. Higher water phosphorus (P) concentrations could also be beneficial for the faster N removal from the waterbodies, which is mediated via the coupled processes regulating the N transfer from water column to anoxic sediments. China has recently issued the "lake-chief" systems, addressing the specific and flexible strategies for water pollution control in different lakes. The self-purification capacity through denitrification and burial rate, which are closely related to WRT, should be taken into consideration when making specific water management plans in the future.

Ecological risk assessment to marine organisms induced by heavy metals in China's coastal waters.

China's coastal environment has been heavily affected by the loading of terrestrial pollutants in recent decades, and quantitative risk assessment is urgently needed to assess the ecological risks of China's coastal environment. We assessed the ecological risks induced by five heavy metals (including Cu, Zn, Pb, Hg and As) in China's coastal waters for three groups of marine organisms (including crustacean, fish and mollusc) based on data obtained from a nationwide unified coastal environment monitoring program consisting of 301 sampling sites. The results show that higher heavy metal concentrations occurred more frequently in the Bohai Sea and in the estuaries of major sea-going rivers. The ecological risks decreased in the following order: Bohai Sea>Yellow Sea>South China Sea>East China Sea. There was generally low ecological risk, but certain hotspots existed near Tianjin and Jinzhou, which had relatively high ecological risks caused by Cu and Zn.

Impacts of sanitation improvement on reduction of nitrogen discharges entering the environment from human excreta in China.

Identifying the sanitation efficacy in reducing contaminations entering the environment is an important step for water pollution controls and developing management strategies to further improve sanitation conditions. With continuous efforts in sanitation improvement during the past decade, reductions in discharges of aquatic nutrients are expected in China. In this study, we estimated the aquatic nitrogen discharges from human excreta in 31 provinces in China during 2006-2014. The results indicated that the nitrogen discharges entering the environment from human excreta are largely determined by both local population and sanitation conditions. In 2014, the nitrogen discharges from human excreta in the rural areas (2118(1219-3140) Gg per year) (median and 95% confidence interval) are higher than those in the urban areas (1485(626-2495) Gg per year). The significant relationship (R2=0.38, n=29) between the total nitrogen concentrations in lakes and corresponding local nitrogen discharges indicated that, the lakes might be potentially affected by the contaminant inputs from human excreta. The further calculations under two policy scenarios showed that through sanitation improvement, further reduction of nitrogen discharges from human excreta in the developed regions might be limited. The sanitation improvement in the less-developed regions, such as Tibet, Qinghai, and Ningxia, should be considered a priority due to the larger reduction potentials.

Nutrient Loads Flowing into Coastal Waters from the Main Rivers of China (2006-2012).

Based on monthly monitoring data of unfiltered water, the nutrient discharges of the eight main rivers flowing into the coastal waters of China were calculated from 2006 to 2012. In 2012, the total load of NH3-N (calculated in nitrogen), total nitrogen (TN, calculated in nitrogen) and total phosphorus (TP, calculated in phosphorus) was 5.1 × 10(5), 3.1 × 10(6) and 2.8 × 10(5) tons, respectively, while in 2006, the nutrient load was 7.4 × 10(5), 2.2 × 10(6) and 1.6 × 10(5) tons, respectively. The nutrient loading from the eight major rivers into the coastal waters peaked in summer and autumn, probably due to the large water discharge in the wet season. The Yangtze River was the largest riverine nutrient source for the coastal waters, contributing 48% of the NH3-N discharges, 66% of the TN discharges and 84% of the TP discharges of the eight major rivers in 2012. The East China Sea received the majority of the nutrient discharges, i.e. 50% of NH3-N (2.7 × 10(5) tons), 70% of TN (2.2 × 10(6) tons) and 87% of TP (2.5 × 10(5) tons) in 2012. The riverine discharge of TN into the Yellow Sea and Bohai Sea was lower than that from the direct atmospheric deposition, while for the East China Sea, the riverine TN input was larger.

CdS nanoflake arrays for highly efficient light trapping.

CdS nanoflake arrays (NFAs) exhibit unprecedented light absorption capability, and they can serve as a scaffold to load thin organic absorbers for extraordinarily high light absorption. As a result, the hybrid solar cell consisting of NFAs and organic absorber yields a ten-times high short-circuit photocurrent compared to the counterpart device with a common planar structure.

[Catalytic degradation of dimethyl sulfoxide in aqueous solutions by liquid-phase pulsed high voltage discharge].

Fenton catalytic degradation of dimethyl sulfoxide (DMSO) by using liquid-phase pulsed high voltage discharge was carried out. The discharge was driven by a self-made pulsed power supply providing a pulse rising time of 400 ns, discharge repetition rate of 96.2 Hz, peak voltage of 20 kV. The side surface of discharge electrode was insulated in order to limit the discharge current, followed by estimating its effect on single pulse power. The effects of aqueous conductivity, Fe(II), and O2 flow rate on liquid-phase discharge induced DMSO degradation and aqueous conductivity on corresponding H2O2 yield were investigated. The concentrations and selectivities of intermediates of DMSO degradation, were also studied. The results indicated that when using the insulated electrode, single pulse power had a limiting value with increasing the aqueous conductivity; DMSO degradation rate was reduced with increasing the aqueous conductivity and O2 flow rate,whereas Fe(II) showed a Fenton catalytic oxidation of DMSO; 80% of DMSO degradation rate was achieved at the pulsed high voltage discharge time of 45 min and the resultant biodegradability was enhanced by at least 32%-48%; the maximum energy efficiency in G(37%) was 0.0087 mol/(kW x h). The study suggested that the liquid-phase plasma combined catalyst promised the potential of organic compound degradation.