Tsunami evacuation is an effective way to save lives from the near-field tsunami. Realistic evacuation simulation can provide valuable information for accurate evacuation risk assessment and ...effective evacuation planning. Agent-based modeling is ideal for tsunami evacuation simulation due to its capability of capturing the emergent phenomena and modeling the individual-level interactions among agents and the agents’ interactions with the environment. However, existing models usually neglect or simplify some important factors and/or mechanisms in tsunami evacuation. For example, uncertainties in seismic damages to the transportation network are not probabilistically considered (e.g., by simply removing the damaged links (roads/bridges) from the network). Typically a relatively small population (i.e., evacuees) is considered (due to computational challenges) while neglecting population mobility. These simplifications may lead to inaccurate estimation of evacuation risk. Usually, only single traffic mode (e.g., on foot or by car) is considered, while pedestrian speed adjustment and multi-modal evacuation (e.g., on foot and by car) are not considered concurrently. Also, pedestrian–vehicle interaction is usually neglected in the multi-modal evacuation. To address the above limitations, this study proposes a novel and more realistic agent-based tsunami evacuation model for tsunami evacuation simulation and risk assessment. Uncertainties in seismic damages to all links in the transportation network as well as uncertainties in other evacuation parameters are explicitly modeled and considered. A novel and more realistic multi-modal evacuation model is proposed that explicitly considers the pedestrian–vehicle interaction, walking speed variability, and speed adjustment for both the pedestrian and car according to traffic density. In addition, several different population sizes are used to model population mobility and its impact on tsunami evacuation risk. The proposed model is applied within a simulation-based framework to assess the tsunami evacuation risk assessment for Seaside, Oregon.
Typically, tsunami evacuation routes are marked using signs in the transportation network and the evacuation map is made to educate people on how to follow the evacuation route. However, tsunami ...evacuation routes are usually identified without the support of evacuation simulation, and the route effectiveness in the reduction of evacuation risk is typically unknown quantitatively. This study proposes a simulation-based and risk-informed framework for quantitative evaluation of the effectiveness of evacuation routes in reducing evacuation risk. An agent-based model is used to simulate the tsunami evacuation, which is then used in a simulation-based risk assessment framework to evaluate the evacuation risk. The route effectiveness in reducing the evacuation risk is evaluated by investigating how the evacuation risk varies with the proportion of the evacuees that use the evacuation route. The impacts of critical risk factors such as evacuation mode (for example, on foot or by car) and population size and distribution on the route effectiveness are also investigated. The evacuation risks under different cases are efficiently calculated using the augmented sample-based approach. The proposed approach is applied to the risk-informed evaluation of the route effectiveness for tsunami evacuation in Seaside, Oregon. The evaluation results show that the route usage is overall effective in reducing the evacuation risk in the study area. The results can be used for evacuation preparedness education and hence effective evacuation.
The objective of this research was to identify single nucleotide polymorphisms (SNPs) and to develop an Illumina Infinium BeadChip that contained over 50,000 SNPs from soybean (Glycine max L. Merr.). ...A total of 498,921,777 reads 35-45 bp in length were obtained from DNA sequence analysis of reduced representation libraries from several soybean accessions which included six cultivated and two wild soybean (G. soja Sieb. et Zucc.) genotypes. These reads were mapped to the soybean whole genome sequence and 209,903 SNPs were identified. After applying several filters, a total of 146,161 of the 209,903 SNPs were determined to be ideal candidates for Illumina Infinium II BeadChip design. To equalize the distance between selected SNPs, increase assay success rate, and minimize the number of SNPs with low minor allele frequency, an iteration algorithm based on a selection index was developed and used to select 60,800 SNPs for Infinium BeadChip design. Of the 60,800 SNPs, 50,701 were targeted to euchromatic regions and 10,000 to heterochromatic regions of the 20 soybean chromosomes. In addition, 99 SNPs were targeted to unanchored sequence scaffolds. Of the 60,800 SNPs, a total of 52,041 passed Illumina's manufacturing phase to produce the SoySNP50K iSelect BeadChip. Validation of the SoySNP50K chip with 96 landrace genotypes, 96 elite cultivars and 96 wild soybean accessions showed that 47,337 SNPs were polymorphic and generated successful SNP allele calls. In addition, 40,841 of the 47,337 SNPs (86%) had minor allele frequencies ≥ 10% among the landraces, elite cultivars and the wild soybean accessions. A total of 620 and 42 candidate regions which may be associated with domestication and recent selection were identified, respectively. The SoySNP50K iSelect SNP beadchip will be a powerful tool for characterizing soybean genetic diversity and linkage disequilibrium, and for constructing high resolution linkage maps to improve the soybean whole genome sequence assembly.
Association analysis is an alternative to conventional family-based methods to detect the location of gene(s) or quantitative trait loci (QTL) and provides relatively high resolution in terms of ...defining the genome position of a gene or QTL. Seed protein and oil concentration are quantitative traits which are determined by the interaction among many genes with small to moderate genetic effects and their interaction with the environment. In this study, a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTL) controlling seed protein and oil concentration in 298 soybean germplasm accessions exhibiting a wide range of seed protein and oil content.
A total of 55,159 single nucleotide polymorphisms (SNPs) were genotyped using various methods including Illumina Infinium and GoldenGate assays and 31,954 markers with minor allele frequency >0.10 were used to estimate linkage disequilibrium (LD) in heterochromatic and euchromatic regions. In euchromatic regions, the mean LD (r2) rapidly declined to 0.2 within 360 Kbp, whereas the mean LD declined to 0.2 at 9,600 Kbp in heterochromatic regions. The GWAS results identified 40 SNPs in 17 different genomic regions significantly associated with seed protein. Of these, the five SNPs with the highest associations and seven adjacent SNPs were located in the 27.6-30.0 Mbp region of Gm20. A major seed protein QTL has been previously mapped to the same location and potential candidate genes have recently been identified in this region. The GWAS results also detected 25 SNPs in 13 different genomic regions associated with seed oil. Of these markers, seven SNPs had a significant association with both protein and oil.
This research indicated that GWAS not only identified most of the previously reported QTL controlling seed protein and oil, but also resulted in narrower genomic regions than the regions reported as containing these QTL. The narrower GWAS-defined genome regions will allow more precise marker-assisted allele selection and will expedite positional cloning of the causal gene(s).
In this paper, Gath–Geva (G–G) fuzzy clustering is extended to adaptively segment hydrometeorological multivariate time series. First, KPCA is used to extract principle components of multivariate ...time series to remove the impacts of redundant and irrelevant variables. Then, taking the time information into account, the segmentation of principle components of multivariate time series is derived with the modified Davies–Bouldin Index and adaptive G–G fuzzy clustering. In the experiment, our proposed algorithm is applied on the real-world hydrometeorological multivariate time series collected every 6 min with length
N
=
720
. Comparison with the existing segmentation algorithms, our proposed algorithm proves the applicability and usefulness in hydrometeorological multivariate time series analysis.
A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was ...primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, the genome positions of these markers need to be mapped.
Two high density genetic linkage maps were constructed based on 21,478 single nucleotide polymorphism loci mapped in the Williams 82 x G. soja (Sieb. & Zucc.) PI479752 population with 1083 RILs and 11,922 loci mapped in the Essex x Williams 82 population with 922 RILs. There were 37 regions or single markers where marker order in the two populations was in agreement but was not consistent with the physical position in the Glyma1.01 build. In addition, 28 previously unanchored scaffolds were positioned. Map data were used to identify false joins in the Glyma1.01 assembly and the corresponding scaffolds were broken and reassembled to the new assembly, Wm82.a2.v1. Based upon the plots of the genetic on physical distance of the loci, the euchromatic and heterochromatic regions along each chromosome in the new assembly were delimited. Genomic positions of the commonly used markers contained in BARCSOYSSR_1.0 database and the SoySNP50K BeadChip were updated based upon the Wm82.a2.v1 assembly.
The information will facilitate the study of recombination hot spots in the soybean genome, identification of genes or quantitative trait loci controlling yield, seed quality and resistance to biotic or abiotic stresses as well as other genetic or genomic research.
This paper introduces a new seismic isolation system called a periodic foundation （PF）, where inclusions are periodically arranged. The PF is different from traditional base isolation in that it ...causes a fundamental frequency shift in the structure, thus reducing its response and generating a frequency gap. If the frequency contents of a seismic wave fall into the gap, it can not propagate in the foundation. Thus, it will exert no influence on the structure above. A systematic study of the band of frequency gap for a 2D PF is conducted. The influence of physical and geometrical parameters such as density and elastic modulus as well as filling fraction of the PF and its materials on the band of frequency gap are investigated, and a design with a frequency gap as low as 2.49-3.72 Hz is achieved. This band of frequency gap corresponds well to the design spectra in earthquake engineering. Numerical simulations of a six-story frame structure with different foundations demonstrate that a proposed PF can greatly reduce the seismic response of an isolated structure. This investigation shows that PFs have great potential in future applications of seismic isolation technology.
The United States Department of Agriculture, Soybean Germplasm Collection includes 18,480 domesticated soybean and 1168 wild soybean accessions introduced from 84 countries or developed in the United ...States. This collection was genotyped with the SoySNP50K BeadChip containing greater than 50K single-nucleotide polymorphisms. Redundant accessions were identified in the collection, and distinct genetic backgrounds of soybean from different geographic origins were observed that could be a unique resource for soybean genetic improvement. We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the wild, landrace, and North American cultivar populations and identified candidate regions associated with domestication and selection imposed by North American breeding. We constructed the first soybean haplotype block maps in the wild, landrace, and North American cultivar populations and observed that most recombination events occurred in the regions between haplotype blocks. These haplotype maps are crucial for association mapping aimed at the identification of genes controlling traits of economic importance. A case-control association test delimited potential genomic regions along seven chromosomes that most likely contain genes controlling seed weight in domesticated soybean. The resulting dataset will facilitate germplasm utilization, identification of genes controlling important traits, and will accelerate the creation of soybean varieties with improved seed yield and quality.
Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were ...to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide (≥7). Among the 61,458 SSRs, (AT)n, (ATT)n and (AAAT)n were the most abundant motifs among di-, tri-, and tetranucleotide SSRs, respectively. After screening for a number of factors including locus-specificity using e-PCR, a soybean SSR database (BARCSOYSSR_1.0) with the genome position and primer sequences for 33,065 SSRs was created. To examine the likelihood that primers in the database would function to amplify locus-specific polymorphic products, 1034 primer sets were evaluated by amplifying DNAs of seven diverse Glycine max (L.) Merr. and one wild soybean (Glycine soja Siebold & Zucc.) genotypes. A total of 978 (94.6%) of the primer sets amplified a single polymerase chain reaction (PCR) product and 798 (77.2%) amplified polymorphic amplicons as determined by 4.5% agarose gel electrophoresis. The BARCSOYSSR1.0 SSR markers can be found in SoyBase (http://soybase.org; verified 21 June 2010) the USDA-ARS Soybean Genome Database.
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