An overview of signal amplification strategies and construction methods on phage-based biosensors.

Phages are a class of viruses that specifically infect host bacteria. Compared to other recognition elements, phages offer several advantages such as high specificity, easy to obtain and good environmental tolerance, etc. These advantages underscore the potential of phages as recognition elements in the construction of biosensors. Therefore, the phage-based biosensors are currently garnering widespread attention for detecting pathogens in recent years. However, the test performance such as detection limit, sensitivity and stability of exicting phage-based biosensors require enhancement. In the design of sensors, the selection of various materials and construction methods significantly influences the test performance of the sensor, and employing appropriate signal amplification strategies and construction methods to devise biosensors based on different principles is an effective strategy to enhance sensor performance. The manuscript primarily focuses on the signal amplification strategies and construction methods employed in phage-based biosensors recent ten years, and summarizes the advantages and disadvantages of different signal amplification strategies and construction methods. Meanwhile, the manuscript discusses the relationship between sensor performance and various materials and construction methods, and reviews the application progress of phage-based electrochemical biosensors in the detection of foodborne bacteria. Furthermore, the manuscript points out the present limitations and the future research direction for the field of phage-based biosensors, so as to provide the reference for developing high-performance phage-based biosensors.

Railway track settlement patterns and control measures for multi-tunnel construction underneath a station track group: a case study.

This paper is based on the proximity engineering project of the Baishiyi tunnel group passing under the Chongqing West Station track group. Considering the train load and the spatial relationship of the tunnel and track groups, the settlement patterns, horizontal displacement, and differential settlement of the tunnel-strata-tracks system during the excavation process are studied through theoretical calculations and numerical simulation methods. The results indicate that the tunnel vault, strata, and track settlement deformation patterns are similar. Throughout the tunnel construction process, the tracks underwent uplift, settlement, and eventually stabilized. The settlement trough formed by the excavation of the three tunnels below the track group has an impact range of 25-145 m. Between 35 and 75 m, the differential settlement of the double track gradually increases with excavation. As the tunnel face reaches 75 m, the track differential settlement gradually converges and tends to stabilize. To minimize the impact of underpass tunnel construction on track groups, it is recommended to use a combination of full-section hole grouting and surface reinforcement grouting for ground reinforcement. Additionally, optimizing the construction parameters, including the step length and primary support closure time, and strengthening the locking anchor can further reduce the impact.

Quality assessment of enzymatic methyl-seq library constructed using crude cell lysate.

Enzymatic methyl-seq (EM-seq), an enzyme-based method, identifies genome-wide DNA methylation, which enables us to obtain reliable methylome data from purified genomic DNA by avoiding bisulfite-induced DNA damage. However, the loss of DNA during purification hinders the methylome analysis of limited samples. The crude DNA extraction method is the quickest and minimal sample loss approach for obtaining useable DNA without requiring additional dissolution and purification. However, it remains unclear whether crude DNA can be used directly for EM-seq library construction. In this study, we aimed to assess the quality of EM-seq libraries prepared directly using crude DNA. The crude DNA-derived libraries provided appropriate fragment sizes and concentrations for sequencing similar to those of the purified DNA-derived libraries. However, the sequencing results of crude samples exhibited lower reference sequence mapping efficiencies than those of the purified samples. Additionally, the lower-input crude DNA-derived sample exhibited a marginally lower cytosine-to-thymine conversion efficiency and hypermethylated pattern around gene regulatory elements than the higher-input crude DNA- or purified DNA-derived samples. In contrast, the methylation profiles of the crude and purified samples exhibited a significant correlation. Our findings indicate that crude DNA can be used as a raw material for EM-seq library construction.

Deformation Mechanism and Control of In-Situ Assembling Caisson Technology in Soft Soil Area under Field Measurement and Numerical Simulation.

With urban space becoming much more crowded, the construction of underground spaces continues to expand to deeper, and the requirements for the large depth and minor deformation in urban engineering construction are getting more urgent. A new kind of in-situ assembling caisson technology (called VSM) is a vertical shaft method (VSM), which excavates the stratum under water with a mechanical arm and assembles the prefabricated caisson segments at the same time. This paper takes the Shanghai Zhuyuan Bailonggang Sewage Connecting Pipe Project as an example, which is the first construction project in the soft soil area, such as Shanghai, and makes a technical analysis of the VSM by comparing the field measurement and numerical simulation. Ground settlements and layered deep displacements were monitored in the field measurement during the VSM construction. It shows that the maximum ground settlement caused by the VSM is 15.2 mm and the maximum horizontal displacement is 3.74 mm. The influence range of the shaft excavation on the ground settlement is about 30 m away from the shaft center. The results demonstrate that the VSM construction has great applicability in the soft soil area. A finite element simulation model of the VSM shaft is established and verified by field measurement. There is a certain error between the traditional theoretical calculation by analogy to the common retaining walls of the deep foundation pit and the measured results, while the simulation results are relatively consistent with field measurements. The reasons for the difference are well-analyzed. Finally, the effects of the VSM construction method on the engineering environment are analyzed, and the suggestions for deformation control in the future are put forward.

Recombination map construction method using ONT sequence.

Although meiotic recombination is a key step shared by eukaryotes, the rate of recombination varies at different taxonomic levels. The construction of high-resolution genome-wide recombination maps will help us understand the variability patterns of recombination rates and their molecular basis. ONT sequencing technology has the characteristics of long read length, high throughput, and reasonable cost, and can be used as a data source for the construction of whole-gene recombination landscapes. In order to construct the genome-wide recombination map of an individual conveniently and accurately, we developed a method to construct the recombination landscape based on the third-generation sequencing technology, Oxford Nanopore Sequencing. Here we detail a step-by-step approach to efficiently and accurately construct genome-wide recombination maps using ONT pooled sequencing data. The main contents include compression homopolymers and alignment; acquisition of high-quality variants; estimation of recombinant molecules by the sliding window method; and construction of recombinant maps. The results of simulation data validation show that our method has high sensitivity and specificity at moderate heterozygous variant density and sequencing depth. This method provides a new way of constructing high-resolution individual genome recombination maps using long read sequences, and has important reference significance for the study of recombination rate variation.

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The ecological corridors considering bird movement characteristics and habitat requirements would mitigate species extinction caused by habitat loss or habitat fragmentation and facilitate species gene dispersal and exchange. These functions may in turn benefit urban residents' physical and mental health as well as appreciation of real estates. Nonetheless, main ecological corridor construction methods developed by foreign scholars have not internally considered the movement and habitat characteristics of birds, while corridor research for birds by domestic scholars have focused on explorations of foreign technical methods yet lacked enough knowledge on studied birds' characteristics. Therefore, there is still much room for improvement in the study of urban ecological corridor construction from the perspective of birds. Based on the analyses of domestic and foreign related research from 1975 to 2020, we identified seven corridor construction methods and three corridor optimization methods within which bird ecology can be integrated. The advantages, drawbacks, and applicable scenarios of all the methods were explored accordingly. Finally, we argued that the develop-ment of computational models, which could not only combine bird species' observation data and spatial movement data with landscape structures but could also possess efficient computation power as well as simulate corridor's ecological benefits, would be a trend for constructing ecological corridor for birds.

Numerical analysis and application of the construction method for the small interval tunnel in the turn line of metro.

The surrounding rock may become unstable or even fall down and the initial support may crack and be destroyed when the construction method of the underground excavation tunnel is not properly selected in the turn line of metro. . A section of the Santunbei turn line of Urumqi Metro Line 1# was taken as the engineering background. The proposed construction method was analyzed by numerical simulation. Numerical analysis shows that the final surface settlement caused by the proposed construction method is 3.0 mm and the horizontal convergence is 3.2 mm. It also turns out that the proposed construction method causes less deformation, and the method can be applied to the construction of the small interval tunnel in the Santunbei turn line of metro. The rationality of the method and numerical model was further verified by comparison between the monitored data of surface settlement, horizontal convergence and vault sinking, and numerical simulation results. Finally, the deformation and stress of the six construction methods were compared. The deformation and stress caused by the six construction methods are almost the same. It indicates that the construction spacing between the left and right tunnels does not affect the safety of tunnel construction. Therefore, the appropriate construction spacing could be selected according to the resource configuration, instead of deformation and stress.

Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases.

Many bacterial-related databases are developed to meet the researchers' needs of analysis and search for a number of bacterial information. However, these databases have different data resources, construction methods, data formats, and analysis tools. It's difficult for researchers to select appropriate databases and analysis tools to promote their researches. In the paper, we compared the contents, construction methods, data sources, update frequency, scope and scale of data, analysis tools, and features of nine famous bacterial databases: CARD, EffectiveDB, MBGD, MPD, PATRCI, PHI-base, VFDB, gcMeta and SILVA, and help researchers to better make better use of these databases. In addition, we also hope this review can help researchers develop a more comprehensive database and better tools to meet the needs of researchers.

Implications of construction method and spatial scale on measures of the built environment.

BACKGROUND: Research surrounding the built environment (BE) and health has resulted in inconsistent findings. Experts have identified the need to examine methodological choices, such as development and testing of BE indices at varying spatial scales. We sought to examine the impact of construction method and spatial scale on seven measures of the BE using data collected at two time points. METHODS: The Children's Environmental Health Initiative conducted parcel-level assessments of 57 BE variables in Durham, NC (parcel N = 30,319). Based on a priori defined variable groupings, we constructed seven mutually exclusive BE domains (housing damage, property disorder, territoriality, vacancy, public nuisances, crime, and tenancy). Domain-based indices were developed according to four different index construction methods that differentially account for number of parcels and parcel area. Indices were constructed at the census block level and two alternative spatial scales that better depict the larger neighborhood context experienced by local residents: the primary adjacency community and secondary adjacency community. Spearman's rank correlation was used to assess if indices and relationships among indices were preserved across methods. RESULTS: Territoriality, public nuisances, and tenancy were weakly to moderately preserved across methods at the block level while all other indices were well preserved. Except for the relationships between public nuisances and crime or tenancy, and crime and housing damage or territoriality, relationships among indices were poorly preserved across methods. The number of indices affected by construction method increased as spatial scale increased, while the impact of construction method on relationships among indices varied according to spatial scale. CONCLUSIONS: We found that the impact of construction method on BE measures was index and spatial scale specific. Operationalizing and developing BE measures using alternative methods at varying spatial scales before connecting to health outcomes allows researchers to better understand how methodological decisions may affect associations between health outcomes and BE measures. To ensure that associations between the BE and health outcomes are not artifacts of methodological decisions, researchers would be well-advised to conduct sensitivity analysis using different construction methods. This approach may lead to more robust results regarding the BE and health outcomes.

Evidence reasoning method for constructing conditional probability tables in a Bayesian network of multimorbidity.

BACKGROUND: The intrinsic mechanism of multimorbidity is difficult to recognize and prediction and diagnosis are difficult to carry out accordingly. Bayesian networks can help to diagnose multimorbidity in health care, but it is difficult to obtain the conditional probability table (CPT) because of the lack of clinically statistical data. OBJECTIVE: Today, expert knowledge and experience are increasingly used in training Bayesian networks in order to help predict or diagnose diseases, but the CPT in Bayesian networks is usually irrational or ineffective for ignoring realistic constraints especially in multimorbidity. METHODS: In order to solve these problems, an evidence reasoning (ER) approach is employed to extract and fuse inference data from experts using a belief distribution and recursive ER algorithm, based on which evidence reasoning method for constructing conditional probability tables in Bayesian network of multimorbidity is presented step by step. RESULTS: A multimorbidity numerical example is used to demonstrate the method and prove its feasibility and application. Bayesian network can be determined as long as the inference assessment is inferred by each expert according to his/her knowledge or experience. CONCLUSIONS: Our method is more effective than existing methods for extracting expert inference data accurately and is fused effectively for constructing CPTs in a Bayesian network of multimorbidity.