In the past many years, some scholars have studied bid evaluation experts, such as the behavior of bid evaluation experts. However, previous research ignores the performance and competency of bid ...evaluation experts, so this paper aims to provide a theoretical basis for incentive and constraint mechanism and hierarchical or dynamic management of bid evaluation experts by implementing performance and dynamic competency evaluation of bid evaluation experts. Firstly, the evaluation index system of performance and dynamic competency of bid evaluation experts is preliminarily constructed by referring to relevant literature, and then the constructed evaluation index was modified and improved by consulting relevant stakeholders' experts. Secondly, considering the hesitation and consistency of expert weighting, the calculation method of expert weight coefficient and index score interval number is improved. Based on the theory of weight interval number, the corresponding mathematical optimization model is constructed to calculate the index weight according to the purpose of performance judgment and dynamic competency clustering of bid evaluation experts. Finally, the data of performance and dynamic competency of bid evaluation experts is obtained by questionnaire survey, and the empirical analysis was carried out by simulating the bid evaluation experts consistent with the actual situation. After improving the calculation method of index score interval number, and then calculating index weight interval number through index score interval number, the length of index weight interval number can be decreased and the calculation accuracy of index weight interval number can be increased. In addition, the index weight calculated by the constructed mathematical optimization model can make the intra-class discrimination smaller and the inter-class discrimination larger. Finally, some suggestions are also provided for the management of bid evaluation experts.
Supporting the translation from natural language (NL) query to visualization (NL2VIS) can simplify the creation of data visualizations because if successful, anyone can generate visualizations by ...their natural language from the tabular data. The state-of-the-art NL2VIS approaches ( e.g. , NL4DV and FlowSense) are based on semantic parsers and heuristic algorithms, which are not end-to-end and are not designed for supporting (possibly) complex data transformations. Deep neural network powered neural machine translation models have made great strides in many machine translation tasks, which suggests that they might be viable for NL2VIS as well. In this paper, we present ncNet , a Transformer-based sequence-to-sequence model for supporting NL2VIS, with several novel visualization-aware optimizations, including using attention-forcing to optimize the learning process, and visualization-aware rendering to produce better visualization results. To enhance the capability of machine to comprehend natural language queries, ncNet is also designed to take an optional chart template ( e.g. , a pie chart or a scatter plot) as an additional input, where the chart template will be served as a constraint to limit what could be visualized. We conducted both quantitative evaluation and user study, showing that ncNet achieves good accuracy in the nvBench benchmark and is easy-to-use.
Insight into high-resolution three-dimensional genome organization and its effect on transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach, we map H3K4me3- and ...RNA polymerase II (RNAPII)-associated promoter-promoter interactions and H3K9me2-marked heterochromatin interactions at nucleotide/gene resolution in rice. The chromatin architecture is separated into different independent spatial interacting modules with distinct transcriptional potential and covers approximately 82% of the genome. Compared to inactive modules, active modules possess the majority of active loop genes with higher density and contribute to most of the transcriptional activity in rice. In addition, promoter-promoter interacting genes tend to be transcribed cooperatively. In contrast, the heterochromatin-mediated loops form relative stable structure domains in chromatin configuration. Furthermore, we examine the impact of genetic variation on chromatin interactions and transcription and identify a spatial correlation between the genetic regulation of eQTLs and e-traits. Thus, our results reveal hierarchical and modular 3D genome architecture for transcriptional regulation in rice.
DNA methylation plays crucial roles in most eukaryotic organisms. Bisulfite sequencing (BS-Seq) is a sequencing approach that provides quantitative cytosine methylation levels in genome-wide scope ...and single-base resolution. However, genomic variations such as insertions and deletions (indels) affect methylation calling, and the alignment of reads near/across indels becomes inaccurate in the presence of polymorphisms. Hence, the simultaneous detection of DNA methylation and indels is important for exploring the mechanisms of functional regulation in organisms.
These problems motivated us to develop the algorithm BatMeth2, which can align BS reads with high accuracy while allowing for variable-length indels with respect to the reference genome. The results from simulated and real bisulfite DNA methylation data demonstrated that our proposed method increases alignment accuracy. Additionally, BatMeth2 can calculate the methylation levels of individual loci, genomic regions or functional regions such as genes/transposable elements. Additional programs were also developed to provide methylation data annotation, visualization, and differentially methylated cytosine/region (DMC/DMR) detection. The whole package provides new tools and will benefit bisulfite data analysis.
BatMeth2 improves DNA methylation calling, particularly for regions close to indels. It is an autorun package and easy to use. In addition, a DNA methylation visualization program and a differential analysis program are provided in BatMeth2. We believe that BatMeth2 will facilitate the study of the mechanisms of DNA methylation in development and disease. BatMeth2 is an open source software program and is available on GitHub ( https://github.com/GuoliangLi-HZAU/BatMeth2 /).
The Fe(3)O(4)@SiO(2)@graphene microspheres were prepared and demonstrated to be highly efficient enrichment materials for proteins and peptides in MALDI-TOF MS analysis.
Mapping seismic structures of sedimentary basins is of great importance to better evaluate energy resources and seismic hazards. In this study, we develop a joint Bayesian Monte Carlo nonlinear ...inversion method that utilizes the complementary nature of Rayleigh wave phase velocity, Rayleigh wave particle motion, and teleseismic P wave in responding to sedimentary structures. Synthetic tests demonstrate that our joint inversion can retrieve the input sedimentary models better than inversions with surface or body wave data alone. We apply our method to waveform data of two broadband stations inside the Songliao Basin in northeast China to invert for sedimentary structures beneath the two stations. We verify our results by successfully isolating the Moho P‐to‐S conversion from sediment reverberations in surface receiver functions with a wavefield‐downward‐continuation technique. We further demonstrate that we can extend our method to single‐station inversions by excluding the Rayleigh wave phase velocity in the inversion.
Key Points
Rayleigh wave phase velocity, particle motion, and teleseismic body wave data are jointly inverted for high‐resolution sedimentary models
The high‐resolution sedimentary models are used to effectively extract deep structural signals by removing sediment reverberations
The method can be extended to single‐station recordings by excluding the Rayleigh wave phase velocity
Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis ...regulation of differentially expressed genes determining ear and tassel architecture within the 3D genome context is largely unknown.
We identify 56,055 and 52,633 open chromatin regions (OCRs) in developing maize ear and tassel primordia using ATAC-seq and characterize combinatorial epigenome features around these OCRs using ChIP-seq, Bisulfite-seq, and RNA-seq datasets. Our integrative analysis of coordinated epigenetic modification and transcription factor binding to OCRs highlights the cis and trans regulation of differentially expressed genes in ear and tassel controlling inflorescence architecture. We further systematically map chromatin interactions at high-resolution in corresponding tissues using in situ digestion-ligation-only Hi-C (DLO Hi-C). The extensive chromatin loops connecting OCRs and genes provide a 3D view on cis- and trans-regulatory modules responsible for ear- and tassel-specific gene expression. We find that intergenic SNPs tend to locate in distal OCRs, and our chromatin interaction maps provide a potential mechanism for trait-associated intergenic SNPs that may contribute to phenotypic variation by influencing target gene expression through chromatin loops.
Our comprehensive epigenome annotations and 3D genome maps serve as valuable resource and provide a deep understanding of the complex regulatory mechanisms of genes underlying developmental and morphological diversities between maize ear and tassel.
Although the correlation between gut microbiota, species identity and geographic locations has long attracted the interest of scientists, to what extent species identity and geographic locations ...influence the gut microbiota assemblages in granivorous rodents needs further investigation. In this study, we performed a survey of gut microbial communities of four rodent species (
,
,
and
) distributed in two areas with great distance (> 600 km apart), to assess if species identity dominates over geographic locations in shaping gut microbial profiles using 16S rRNA gene sequencing. We found that gut microbiota composition varied significantly across host species and was closely correlated with host genetics. We identified strong species identity effects on gut microbial composition, with a comparatively weaker signal of geographic provenance on the intestinal microbiota. Specifically, microbiota of one species was on average more similar to that of conspecifics living in separate sites than to members of a closely related species living in the same location. Our study suggests that both host genetics and geographical variations influence gut microbial diversity of four rodent species, which merits further investigation to reveal the patterns of phylogenetic correlation of gut microbial community assembly in mammals across multiple habitats.
Scheme for preparation of GSH-Au NCs (a) and application in selective determination of Cr(III) and Cr(VI) (b). Display omitted
► Facile and rapid preparation of fluorescent glutathione-stabilized ...gold nanoclusters. ► New method for selective determination of Cr(III) and Cr(VI) using GSH-Au NCs. ► The detection method possessed simplicity, high throughput, high selectivity and sensitivity.
A novel method for selective determination of Cr(III) and Cr(VI) in environmental water samples was developed based on target-induced fluorescence quenching of glutathione-stabilized gold nanoclusters (GSH-Au NCs). Fluorescent GSH-Au NCs were synthesized by a one-step approach employing GSH as reducing/protecting reagent. It was found that Cr(III) and Cr(VI) showed pH-dependent fluorescence quenching capabilities for GSH-Au NCs, and thus selective determination of Cr(III) and Cr(VI) could be achieved at different pHs. Addition of EDTA was able to effectively eliminate the interferences from other metal ions, leading to a good selectivity for this method. Under optimized conditions, Cr(III) showed a linear range of 25–3800μgL−1 and a limit of detection (LOD) of 2.5μgL−1. The Cr(VI) ion demonstrated a linear range of 5–500μgL−1 and LOD of 0.5μgL−1. The run-to-run relative standard deviations (n=5) for Cr(III) and Cr(VI) were 3.9% and 2.8%, respectively. The recoveries of Cr(III) and Cr(VI) in environmental water samples were also satisfactory (76.3–116%). This method, with its simplicity, low cost, high selectivity and sensitivity, could be used as a promising tool for chromium analysis in environmental water samples.
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