Streptococcus suis Sequence Type 7 Outbreak, Sichuan, China

An outbreak of Streptococcus suis serotype 2 emerged in the summer of 2005 in Sichuan Province, and sporadic infections occurred in 4 additional provinces of China. In total, 99 S. suis strains were isolated and analyzed in this study: 88 isolates from human patients and 11 from diseased pigs. We defined 98 of 99 isolates as pulse type I by using pulsed-field gel electrophoresis analysis of SmaI-digested chromosomal DNA. Furthermore, multilocus sequence typing classified 97 of 98 members of the pulse type I in the same sequence type (ST), ST-7. Isolates of ST-7 were more toxic to peripheral blood mononuclear cells than ST-1 strains. S. suis ST-7, the causative agent, was a single-locus variant of ST-1 with increased virulence. These findings strongly suggest that ST-7 is an emerging, highly virulent S. suis clone that caused the largest S. suis outbreak ever described

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio

An Expanded Evaluation of Protein Function Prediction Methods Shows an Improvement In Accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

Optimal Manufacturer Recycling Strategy under EPR Regulations

Under extended producer responsibility (EPR) regulations, trade-in programs allow manufacturers to play a vital role in recycling. Simultaneously, third-party recyclers (TPRs) can use their recycling network to compensate for manufacturers having only a single recycling channel, which increases the competition between them. To study whether companies should authorize TPRs, we constructed and analyzed a Stackelberg game model with trade-in programs under EPR regulations by focusing on three different closed-loop supply chain (CLSC) structures and differentiating consumer categories. The analytical results showed that when the government does not act as the decision maker, the optimal product selling price of the manufacturer does not change under each strategy. Otherwise, the manufacturer’s decision is affected by the cost structure and amount of subsidy, as well as funds determined by the government under the optimal environmental benefit. Furthermore, when the residual value coefficient of the used products is high, manufacturers authorize TPRs to recycle used products

Effects of litter and root manipulations on soil carbon and nitrogen in a Schrenk's spruce (Picea schrenkiana) forest.

Plant detritus represents the major source of soil carbon (C) and nitrogen (N), and changes in its quantity can influence below-ground biogeochemical processes in forests. However, we lack a mechanistic understanding of how above- and belowground detrital inputs affect soil C and N in mountain forests in an arid land. Here, we explored the effects of litter and root manipulations (control (CK), doubled litter input (DL), removal of litter (NL), root exclusion (NR), and a combination of litter removal and root exclusion (NI)) on soil C and N concentrations, enzyme activity and microbial biomass during a 2-year field experiment. We found that DL had no significant effect on soil total organic carbon (SOC) and total nitrogen (TN) but significantly increased soil dissolved organic carbon (DOC), microbial biomass C, N and inorganic N as well as soil cellulase, phosphatase and peroxidase activities. Conversely, NL and NR reduced soil C and N concentrations and enzyme activities. We also found an increase in the biomass of soil bacteria, fungi and actinomycetes in the DL treatment, while NL reduced the biomass of gram-positive bacteria, gram-negative bacteria and fungi by 5.15%, 17.50% and 14.17%, respectively. The NR decreased the biomass of these three taxonomic groups by 8.97%, 22.11% and 21.36%, respectively. Correlation analysis showed that soil biotic factors (enzyme activity and microbial biomass) and abiotic factors (soil moisture content) significantly controlled the change in soil C and N concentrations (P < 0.01). In brief, we found that the short-term input of plant detritus could markedly affect the concentrations and biological characteristics of the C and N fractions in soil. The removal experiment indicated that the contribution of roots to soil nutrients is greater than that of the litter

Complementary Feeding and Malnutrition among Infants and Young Children Aged 6&ndash;23 Months in Rural Areas of China

This study investigated the nutrition and complementary feeding (CF) of infants and young children (IYC) aged 6&ndash;23 months in rural areas of China in 2018 and explored the relationship between CF and nutritional status. We measured the length and weight, calculated the z-scores, and detected micronutrients in the hair. The status of CF was obtained from the respondents by a 24-h dietary recall. IYC were classified into clusters using a two-step cluster analysis. The CF and nutritional status of each cluster were analyzed and compared. The prevalence of stunting, wasting, and overweight in the IYC in rural Chinese areas was 7.1%, 3.0%, and 3.7%, respectively. The median levels of Ca, Fe, and Zn in hair were 550.10 &micro;g/g, 62.94 &micro;g/g, and 132.86 &micro;g/g, respectively. The prevalence of meeting the requirements of minimum dietary diversity (MDD), minimum meal frequency (MMF), and minimum acceptable diet (MAD) was 68.9%, 77.9%, and 46.4%, respectively. IYC with a higher prevalence of MDD, MMF, and MAD were more inclined to maintain a healthy status. The prevalence of undernutrition and overweight of 6- to 23-month-old IYC in rural areas of China was low. However, lack of trace elements was evident, and MAD prevalence remained low

Changes in Soil Microbial Communities under Mixed Organic and Inorganic Nitrogen Addition in Temperate Forests

Investigating the response of soil microbial communities to nitrogen (N) deposition is critical to understanding biogeochemical processes and the sustainable development of forests. However, whether and to what extent different forms of N deposition affect soil microbial communities in temperate forests is not fully clear. In this work, a field experiment with three years of simulated nitrogen deposition was conducted in temperate forests. The glycine and urea were chosen as organic nitrogen (ON) source, while NH4NO3 was chosen as inorganic nitrogen (IN) source. Different ratios of ON to IN (CK = 0:0, Mix-1 = 10:0, Mix-2 = 7:3, Mix-3 = 5:5, Mix-4 = 3:7, Mix-5 = 0:10) were mixed and then used with equal total amounts of 10 kg·N·ha−1·a−1. We determined soil microbial diversity and community composition for bacteria and fungi (16S rRNA and ITS), and soil parameters. Different forms of N addition significantly changed the soil bacterial and fungal communities. Mixed N sources had a positive effect on soil bacterial diversity and a negative effect on fungal diversity. Bacterial and fungal community structures were significantly separated under different forms of N addition. Soil pH was the main factor affecting the change in fungal community structure, while bacterial community structure was mainly controlled by STN. We also found that Proteobacteria, Acidobacteriota, Basidiomycota and Ascomycota were the most abundant phyla, regardless of the form of N addition. RDA showed that C/P and NH4+ were the main factors driving the change in bacterial community composition, and C/P, pH and C/N were the main factors driving the change in fungal community composition. Our results indicate that different components of N deposition need to be considered when studying the effects of N deposition on soil microorganisms in terrestrial ecosystems

Effects of the Duration of Ying Yang Bao Consumption on Hemoglobin Concentration in Infants and Young Children in Less Developed Areas of China

Ying Yang Bao (YYB) is conventionally prescribed as a nutritional supplement to infants and young children (IYC) in less developed areas of China. However, whether 18-month YYB consumption is reasonable needs assessment. This study examined the influence of the duration of YYB consumption on hemoglobin (Hb) levels and anemia prevalence. Data from the Nutrition Improvement Project on Children in Poor Areas of China in 2018&ndash;2019 were used. Questionnaires were used to collect information on basic characteristics, dietary status, and YYB consumption. Propensity score matching (PSM) was used to balance confounders. Hb levels and anemia prevalence in IYC with different durations of YYB consumption were compared. After PSM, all covariates were well-balanced, and 1151 pairs of IYC were included in subsequent analyses. During the 1st&ndash;9th months of intervention, YYB effectively increased Hb levels and reduced anemia prevalence in the intervention group. During the 10th&ndash;18th months of intervention, Hb levels in the control group increased and anemia prevalence decreased, while Hb levels and anemia prevalence fluctuated in the intervention group. In conclusion, YYB was effective in improving nutritional status of infants, but had a limited effect in young children. Nutritional supplements with different quantities or nutrients should be considered for young children

Response of litter decomposition and the soil environment to one-year nitrogen addition in a Schrenk spruce forest in the Tianshan Mountains, China.

Human activities have increased the input of nitrogen (N) to forest ecosystems and have greatly affected litter decomposition and the soil environment. But differences in forests with different nitrogen deposition backgrounds. To better understand the response of litter decomposition and soil environment of N-limited forest to nitrogen deposition. We established an in situ experiment to simulate the effects of N deposition on soil and litter ecosystem processes in a Picea schrenkiana forest in the Tianshan Mountains, China. This study included four N treatments: control (no N addition), low N addition (LN: 5&nbsp;kg&nbsp;N&nbsp;ha-1&nbsp;a-1), medium N addition (MN: 10&nbsp;kg&nbsp;N&nbsp;ha-1&nbsp;a-1) and high N addition (HN: 20&nbsp;kg&nbsp;N&nbsp;ha-1&nbsp;a-1). Our results showed that N addition had a significant effect on litter decomposition and the soil environment. Litter mass loss in the LN treatment and in the MN treatment was significantly higher than that in the control treatment. In contrast, the amount of litter lost in the HN treatment was significantly lower than the other treatments. N application inhibited the degradation of lignin but promoted the breakdown of cellulose. The carbon (C), N, and phosphorus (P) contents of litter did not differ significantly among the treatments, but LN promoted the release of C and P. Our results also showed that soil pH decreased with increasing nitrogen application rates, while soil enzyme activity showed the opposite trend. In addition, the results of redundancy analysis (RDA) and correlation analyses showed that the soil environment was closely related to litter decomposition. Soil enzymes had a positive effect on litter decomposition rates, and N addition amplified these correlations. Our study confirmed that N application had effects on litter decomposition and the soil environment in a N-limited P. schrenkiana forest. LN had a strong positive effect on litter decomposition and the soil environment, while HN was significantly negative. Therefore, increased N deposition may have a negative effect on material cycling of similar forest ecosystems in the near future