A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data

Publisher's PDFBACKGROUND: DNA methylation is an epigenetic modification that plays important roles on gene regulation. Study of whole-genome bisulfite sequencing and reduced representation bisulfite sequencing brings the availability of DNA methylation at single CpG resolution. The main interest of study on DNA methylation data is to test the methylation difference under two conditions of biological samples. However, the high cost and complexity of this sequencing experiment limits the number of biological replicates, which brings challenges to the development of statistical methods. RESULTS: Bayesian modeling is well known to be able to borrow strength across the genome, and hence is a powerful tool for high-dimensional- low-sample- size data. In order to provide accurate identification of methylation loci, especially for low coverage data, we propose a full Bayesian partition model to detect differentially methylated loci under two conditions of scientific study. Since hypo-methylation and hyper-methylation have distinct biological implication, it is desirable to differentiate these two types of differential methylation. The advantage of our Bayesian model is that it can produce one-step output of each locus being either equal-, hypo- or hyper-methylated locus without further post-hoc analysis. An R package named as MethyBayes implementing the proposed full Bayesian partition model will be submitted to the bioconductor website upon publication of the manuscript. CONCLUSIONS: The proposed full Bayesian partition model outperforms existing methods in terms of power while maintaining a low false discovery rate based on simulation studies and real data analysis including bioinformatics analysis.University of Delaware. Department of Applied Economics and Statistics

Effects of vaccines on clinical characteristics of convalescent adult patients infected with SARS-CoV-2 Omicron variant: A retrospective study

IntroductionThe protective effect of SARS-CoV-2 vaccines has become a global focus due to Omicron variant pandemic. The effects of various SARS-CoV-2 vaccines are diverse. However, studies on the effect of domestic vaccines on clinical characteristics in convalescent adult patients infected with the Omicron variant are lacking.MethodsIn this retrospective, single-center cohort study, the effect of three domestic vaccines on clinical characteristics of convalescent adult patients infected with the Omicron variant was investigated in the initial largest outbreak of the Omicron variant infection between January and February 2022 in Tianjin, China. The primary endpoint was COVID-19 severity and the secondary endpoints were re-positive results on nucleic acid tests, liver and kidney function, and inflammation levels during recovery.ResultsA total of 320 adult patients infected with the Omicron variant were enrolled, including 296 post-vaccination and 24 unvaccinated patients. The median age of the unvaccinated patients was higher than that of vaccinated patients, but no significant difference was detected in the sex composition ratio between the different groups. Binary logistic regression results suggested that Sinopharm and Sinovac vaccine was an independent protective factor for relieving the severity of the Omicron variant infection. Regrettably, the vaccines did not showed any protective effect on the liver and kidney function of convalescent adult patients. Three domestic vaccines significantly relieved inflammation and increased the SARS-CoV-2-specific antibody levels. Furthermore, Sinovac and CanSino vaccines had a better immune stimulation effect on increasing T lymphocytes levels in convalescent adult patients. In addition, three domestic vaccines have protective effects on preventing re-detectable positive (RP) result in convalescent adult patients.ConclusionAlthough the three domestic vaccines cannot prevent the infection of the Omicron variant, it has a significant protective effect in adult patients. This study supports the policy of accelerating to vaccination worldwide combat the evolving and mutating SARS-CoV-2.DiscussionOmicron spreads faster and might escape antibodies more readily than previous variants, increasing the cases of reinfection and breakthrough infections in vaccinated people. Although vaccinated people are likely to have a much lower risk of severe disease from Omicron infection, many issues still need to be considered. Concerns about lower vaccine efficacy because of new variants might have changed our understanding of the COVID-19 endgame, disabusing the world of the notion that global vaccination is by itself adequate for controlling SARS-CoV-2 infection. The current data showed that vaccination with three domestic SARS-CoV-2 vaccines alleviates the disease severity of adult patients with COVID-19, reduces the inflammation level and the RP rate of convalescent adult patients, and enhances body’s defense against the virus in convalescent adult patients. Moreover, our study has highlighted that a combination prevention approach of vaccination and public health measures would be an effective strategy

Establishment of a Multiplex Real-Time PCR Method for Detection of Four Plant-Derived Components and Its Application to Edible Starches

A multiplex real-time polymerase chain reaction (PCR) method for simultaneous and rapid detection of components derived from sweet potato, cassava, potato, and corn was established. The g3pdhs gene of sweet potato and cassava, the UGPase gene of potato and the zSSIIb gene of corn were used as target genes to design specific primers and TaqMan probe, and the 18S rRNA gene was used as the internal reference gene. Methodological validation was performed, and the proposed method was applied to simulated samples with different mixing ratios and actual starch samples. The results showed that this method was high-throughput, sensitive and specific. No cross-reaction was found with 15 non-target sources. The detection sensitivity for template DNA was 3 × 10-3 ng/μL, and the proposed method had a good linear relationship and high amplification efficiency. The detection limit for edible starch samples was 0.1%. The results of the PCR method for 50 actual samples were consistent with those of the reference method, indicating that this method could be used for the detection of common adulterants in edible starches

Optimal dispatch based on prediction of distributed electric heating storages in combined electricity and heat networks

The volatility of wind power generations could significantly challenge the economic and secure operation of combined electricity and heat networks. To tackle this challenge, this paper proposes a framework of optimal dispatch with distributed electric heating storage based on a correlation-based long short-term memory prediction model. The prediction model of distributed electric heating storage is developed to model its behavior characteristics which are obtained by the autocorrelation and correlation analysis with external factors including weather and time-of-use price. An optimal dispatch model of combined electricity and heat networks is then formulated and resolved by a constraint reduction technique with clustering and classification. Our method is verified through numerous simulations. The results show that, compared with the state-of-the-art techniques of support vector machine and recurrent neural networks, the mean absolute percentage error with the proposed correlation-based long short-term memory can be reduced by 1.009 and 0.481 respectively. Compared with conventional method, the peak wind power curtailment with dispatching distributed electric heating storage is reduced by nearly 30% and 50% in two cases respectively

Crystal structure of 2-(2-naphthyl)-4,6-dimethylpyrimidine, C(16)H(14)N(2)

C(16)H(14)N(2), monoclinic, P12(1)/c1 (no. 14), a = 8.387(1) angstrom, b = 17.453(3) angstrom, c = 8.694(1) angstrom, beta = 93.092(2)degrees, V = 1270.8 angstrom(3), Z = 4, R(gt)(F) = 0.046, wR(ref)(F(2)) = 0.129, T = 294 K.program for innovation of science and technology talents of Henan Province[104200510022]; program for science and technology leaders of Zhengzhou City[10LJRC174]; Doctor Foundation[D09004]; program for innovative research team of Henan Institute of Engineering[2009IRTHNIE05

The archaeometry and archaeology of ancient Chinese glass: a review

This paper provides a new review of archaeometric research carried out on glass found in China, set in an archaeological context, from its earliest occurrence, to the Song dynasty. It is set within a broad geographical context taking the terrestrial and maritime Silk Road contacts into account. We discuss chemical and isotopic compositional contrasts in glasses from different periods found in different parts of China, the glasses that were almost certainly made in China and those that were imported. A theme that runs through the paper is the problem of provenancing glass found in China. We discuss the glass artefacts that are of typical Chines types and contrast these with imports. The structure reflects the contrast between imported and Chinese made with glasses. We discuss potential new scientific and archaeological approaches to Chinese glass

Taxonomic study of the genus Macquartia Robineau-Desvoidy (Diptera, Tachinidae) from China

The genus Macquartia Robineau-Desvoidy (Diptera, Tachinidae) with 29 known species is a large group of Macquartiini of Tachininae and widely distributed in the Old World and the Nearctic Region.In this study, Chinese specimens of Macquartia were collected and examined, sixteen species are recognised: thirteen previously described, M. brunneisqua Zhang et Li, M. chinensis Zhang et Li, M. flavifemorata Zhang et Li, M. flavipedicel Zhang et Li, M. chalconota (Meigen), M. dispar (Fallén), M. grisea (Fallén), M. macularis Villeneuve, M. nudigena Mesnil, M. picta (Meigen), M. pubiceps (Zetterstedt), M. tenebricosa (Meigen) and M. viridana Robineau-Desvoidy and three species new to science, M. barkamensis sp. n. (Sichuan), M. setifacies sp. n. (Qinghai) and M. sichuanensis sp. n. (Sichuan). An identification key to the sixteen species of Macquartia known from China is included, along with 80 anatomical figures

Multi-dimensional value evaluation for power-to-hydrogen technology based on fuzzy analytic hierarchy process

At present, the large-scale development of renewable energy is restricted by the absorption problem. The electric-hydrogen technology becomes a new flexible resource for coupling electric energy, heat energy and other kinds of energy by absorbing abandoned electricity. The lack of flexibility in a power system with high proportion of intermittent renewables can lead to issues like large-scale curtailment of wind and solar, uneconomic energy system operation; even endanger the security of energy supply. As a new flexible resource, power-to-hydrogen technology has received widespread attention and also requires a comprehensive assessment. The electricity-to-hydrogen technology has become a new flexible resource for coupling electric energy, thermal energy and other energy sources by absorbing and discarding electricity. To this end, this paper proposes a multi-dimensional system value evaluation method for the power-to-hydrogen (P2H) technology, the collaborative planning of large-scale electric-hydrogen resources in the new power system is an important issue in this study. The method, based a fuzzy analytic hierarchy process, delivers a multi-dimensional index that involves a P2H’s flexibility, ability to consume intermittent renewables, economy and environmental value. The system value of P2H and the effectiveness of the proposed algorithm are demonstrated by a use case study. The effects caused by P2H capacity variation are quantified, and an optimal capacity of P2H was found