Search

Abstract Background The emergency of new COVID-19 variants over the past three years posed a serious challenge to the public health. Cities in China implemented mass daily RT-PCR tests by pooling strategies. However, a random delay exists between an infection and its first positive RT-PCR test. It is valuable for disease control to know the delay pattern and daily infection incidences reconstructed from RT-PCR test observations. Methods We formulated the convolution model between daily incidences and positive RT-PCR test counts as a linear inverse problem with positivity restrictions. Consequently, the Richard-Lucy deconvolution algorithm was used to reconstruct COVID-19 incidences from daily PCR tests. A real-time deconvolution was further developed based on the same mathematical principle. The method was applied to an Omicron epidemic data set of a bar outbreak in Beijing and another in Wuxi in June 2022. We estimated the delay function by maximizing likelihood via an E-M algorithm. Results The delay function of the bar-outbreak in 2022 differs from that reported in 2020. Its mode was shortened to 4 days by one day. A 95% confidence interval of the mean delay is [4.43,5.55] as evaluated by bootstrap. In addition, the deconvolved infection incidences successfully detected two associated infection events after the bar was closed. The application of the real-time deconvolution to the Wuxi data identified all explosive incidence increases. The results revealed the progression of the two COVID-19 outbreaks and provided new insights for prevention and control strategies, especially for the role of mass daily RT-PCR testing. Conclusions The proposed deconvolution method is generally applicable to other infectious diseases if the delay model can be assumed to be approximately valid. To ensure a fair reconstruction of daily infection incidences, the delay function should be estimated in a similar context in terms of virus variant and test protocol. Both the delay estimate from the E-M algorithm and the incidences resulted from deconvolution are valuable for epidemic prevention and control. The real-time feedback is particularly useful during the epidemic’s acute phase because it can help the local disease control authorities modify the control measures more promptly and precisely.

Abstract Background Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer representation by the de Bruijn graph or the overlap-layout-consensus paradigm. Besides, chimeric reads will cause erroneous k-mers in the former and false overlaps of reads in the latter. Results We propose a novel local assembly approach to gap closing, called RegCloser. It represents read coordinates and their overlaps respectively by parameters and observations in a linear regression model. The optimal overlap is searched only in the restricted range consistent with insert sizes. Under this linear regression framework, the local DNA assembly becomes a robust parameter estimation problem. We solved the problem by a customized robust regression procedure that resists the influence of false overlaps by optimizing a convex global Huber loss function. The global optimum is obtained by iteratively solving the sparse system of linear equations. On both simulated and real datasets, RegCloser outperformed other popular methods in accurately resolving the copy number of tandem repeats, and achieved superior completeness and contiguity. Applying RegCloser to a plateau zokor draft genome that had been improved by long reads further increased contig N50 to 3-fold long. We also tested the robust regression approach on layout generation of long reads. Conclusions RegCloser is a competitive gap-closing tool. The software is available at https://github.com/csh3/RegCloser . The robust regression approach has a prospect to be incorporated into the layout module of long read assemblers.

Background Measles outbreaks often require labor- and resource-intense response. A border-area measles outbreak occurred in Yunnan province that required outbreak response immunization for its containment. We report results of our investigation into the outbreak and the health sector costs of the response activities, with the goal of providing evidence for policy makers when considering the full value of vaccines and of measles elimination. Methods We conducted case investigations to determine sources of infection and routes of transmission. Costs of outbreak response activities incurred by health sector were determined through retrospective interviews and record reviews of staff. Results In total, 67 measles cases were confirmed, including 4 cases imported from Myanmar. Among the 33 cases aged between 8 months and 14 y old, 22 (66∙7%) had received 2 doses of MCV; 2 (6∙0%) had received 1 dose of MCV; 9 (27∙3%) had not received MCV. The first 4 cases had been infected in Myanmar, and we identified 8 transmission clusters with a total of 62 cases. Transmission among Yunnan province residents occurred in schools, family settings, and at gatherings. The overall cost to control the outbreak was $214,774, for a per-case cost of $3,206. The outbreak response vaccination campaign accounted for 64% of the total outbreak costs. Conclusions Despite high population immunity among Yunnan province children and adolescents, an import-related measles outbreak occurred among individuals who were not vaccinated or had vaccine failure in the across-border area. The economic cost of the outbreak was substantial. Investment in a sensitive measles surveillance system to detect outbreaks in a timely manner, maintaining high population immunity to measles, and reinforcing cross-border collaboration with neighboring countries support achieving and sustaining measles elimination in the border areas of China.

Urban parks provide multiple benefits to human well-being and human health. Big data provide new and powerful ways to study visitors’ feelings, activities in urban parks, and the effect they themselves have on urban parks. However, the term “big data” has been defined variably, and its applications on urban parks have so far been sporadic in research. Therefore, a comprehensive review of big data-based urban park research is much needed. The review aimed to summarize the big data-based urban park research in visitor dimension by a systematic review approach in combination with bibliometric and thematic analyses. The results showed that the number of publications of related articles has been increasing exponentially in recent years. Users’ days data is used most frequently in the big data-based urban park research, and the major analytical methods are of four types: sentiment analysis, statistical analysis, and spatial analysis. The major research topics of big data-based urban park research in visitor dimension include visitors’ behavior, visitors’ perception and visitors’ effect. Big data benefits urban park research by providing low-cost, timely information, a people-oriented perspective, and fine-grained site information. However, its accuracy is insufficient because of coordinate, keyword classification and different kinds of users. To move forward, future research should integrate multiple big data sources, expand the application, such as public health and human–nature interactions, and pay more attention to the big data use for overcoming pandemic. This review can help to understand the current situation of big data-based urban park research, and provide a reference for the studies of this topic in the future.

To solve the problems of small flow and low efficiency for a reciprocating piston pump, a new type of rotary piston pump, triangular rotor pump (TRP), is proposed. Its mechanical structure and working principles are introduced and a mathematical model of the key pump structure and the design requirements for the key sealed components are presented. Experiments involving different outlet sizes and shaft speeds are performed on the AB-1.25D-type TRP. Through Fluent numerical calculation, the fluid flow line, velocity vector, and pressure distribution inside the TRP are analyzed. The results show that, for outlet size a (b) and 190(160)-r/min speed, the pump flow rate reaches a maximum of 8.83 (7.34) m3/h, the shaft power is 5.2 (5.1) kW, and the total efficiency exceeds 72%(65.7%). The numerical calculation results show that four vortices appear in the working-chamber (W-C) for different working processes and areas. The W-C pressure first increases and then decreases, and the maximum pressure occurs at the beginning of the stable full-pressure state. The experimental results for the pressure coefficient, flow coefficient, and total efficiency agree well with the numerical results. The TRP exhibits good performance and can be used in deep mine drainage, long-distance pipeline transportation, and grouting.

This paper investigates the effect of two different welding methods, direct welding (DW) and vacuum furnace welding (VFW), on flip-chip light-emitting diode (FC-LED) filament properties. Shearing force, SEM, steady-state voltage, steady-state luminous flux, and change of photoelectric performance with aging time were employed to characterize the differences in filament properties between the two welding methods. The shearing test revealed that the average shearing force of the VFW group was higher than that of the DW group, but the two groups followed the standard. Furthermore, the microstructure of the VFW group fault was more smoother, and the voids were fewer and smaller based on the SEM test results. The steady-state voltage and luminous flux revealed that the VFW group had a more concentrated voltage and a higher luminous flux. The aging data revealed that the steady-state voltage change rate of both groups was not very different, and both luminous flux maintenance rates of the VFW group were higher than those of the DW group, but all were within the standard range. In conclusion, if there is a higher requirement for filament in a practical application, such as the filament is connected in series or in parallel and needs a higher luminous flux, it can be welded using vacuum furnace welding. If the focus is on production efficiency and the high performance of filaments is not required, direct welding can be used.

In recent years, eutectic high entropy alloys have been found to have excellent mechanical properties and corrosion resistance; however, the simultaneous achievement of these mechanical properties and high-temperature oxidation resistance still constitutes a tough challenge. In this study, Ta and Cr elements are added to (FeCoNiNb)98Al2 high-entropy alloy to improve oxidation resistance, and the changes in microstructure and mechanical properties of (FeCoNiNb)98-2x(TaCr)xAl2 as well as the oxidation behaviors at 900 °C are systematically investigated. The results show that the addition of Ta and Cr elements promotes the increase and growth of the Laves phase in the alloy, which improves the oxidation resistance of the alloy and maintains the excellent mechanical properties of (FeCoNiNb)98Al2. The formation of CrTaO4, CrNbO4, and Cr2O3 composite oxide scales can not only prevent the diffusion of O into the alloy, but also inhibit the external diffusion of matrix elements. This result provide experimental data and theoretical support for the optimal design of the high-entropy alloy compositions to improve their antioxidant properties while maintaining excellent mechanical properties.