This paper proposes the hybrid NM-PSO algorithm based on the Nelder–Mead (NM) simplex search method and particle swarm optimization (PSO) for unconstrained optimization. NM-PSO is very easy to ...implement in practice since it does not require gradient computation. The modification of both the Nelder–Mead simplex search method and particle swarm optimization intends to produce faster and more accurate convergence. The main purpose of the paper is to demonstrate how the standard particle swarm optimizers can be improved by incorporating a hybridization strategy. In a suite of 20 test function problems taken from the literature, computational results via a comprehensive experimental study, preceded by the investigation of parameter selection, show that the hybrid NM-PSO approach outperforms other three relevant search techniques (
i.e., the original NM simplex search method, the original PSO and the guaranteed convergence particle swarm optimization (GCPSO)) in terms of solution quality and convergence rate. In a later part of the comparative experiment, the NM-PSO algorithm is compared to various most up-to-date cooperative PSO (CPSO) procedures appearing in the literature. The comparison report still largely favors the NM-PSO algorithm in the performance of accuracy, robustness and function evaluation. As evidenced by the overall assessment based on two kinds of computational experience, the new algorithm has demonstrated to be extremely effective and efficient at locating best-practice optimal solutions for unconstrained optimization.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Abstract Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived small interfering RNAs has proven ...to be a highly efficient approach for virus discovery. Here we present VirusDetect, a bioinformatics pipeline that can efficiently analyze large-scale small RNA (sRNA) datasets for both known and novel virus identification. VirusDetect performs both reference-guided assemblies through aligning sRNA sequences to a curated virus reference database and de novo assemblies of sRNA sequences with automated parameter optimization and the option of host sRNA subtraction. The assembled contigs are compared to a curated and classified reference virus database for known and novel virus identification, and evaluated for their sRNA size profiles to identify novel viruses. Extensive evaluations using plant and insect sRNA datasets suggest that VirusDetect is highly sensitive and efficient in identifying known and novel viruses. VirusDetect is freely available at http://bioinfo.bti.cornell.edu/tool/VirusDetect/.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Seed plants have evolved to maintain the dormancy of freshly matured seeds until the appropriate time for germination. Seed dormancy and germination are distinct physiological processes, and the ...transition from dormancy to germination is not only a critical developmental step in the life cycle of plants but is also impor- tant for agricultural production. These processes are precisely regulated by diverse endogenous hormones and environmental cues. Although ABA （abscisic acid） and GAs （gibberellins） are known to be the primary phytohormones that antagonistically regulate seed dormancy, recent findings demonstrate that another phytohormone, auxin, is also critical for inducing and maintaining seed dormancy, and therefore might act as a key protector of seed dormancy. In this review, we summarize our current understanding of the sophisticated molecular networks involving the critical roles of phytohormones in regulating seed dormancy and germination, in which AP2-domain-containing transcription factors play key roles. We also discuss the interactions （crosstalk） of diverse hormonal signals in seed dormancy and germination, focusing on the ABA/GA balance that constitutes the central node.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Tobamoviruses, including tomato brown rugose fruit virus (ToBRFV) on tomato and pepper, and cucumber green mottle mosaic virus (CGMMV) on cucumber and watermelon, have caused many disease outbreaks ...around the world in recent years. With seed-borne, mechanical transmission and resistant breaking traits, tobamoviruses pose serious threat to vegetable production worldwide. With the absence of a commercial resistant cultivar, growers are encouraged to take preventative measures to manage those highly contagious viral diseases. However, there is no information available on which disinfectants are effective to deactivate the virus infectivity on contaminated hands, tools and equipment for these emerging tobamoviruses. The purpose of this study was to evaluate a collection of 16 chemical disinfectants for their effectiveness against mechanical transmission of two emerging tobamoviruses, ToBRFV and CGMMV.
Bioassay was used to evaluate the efficacy of each disinfectant based on virus infectivity remaining in a prepared virus inoculum after three short exposure times (10 s, 30 s and 60 s) to the disinfectant and inoculated mechanically on three respective test plants (ToBRFV on tomato and CGMMV on watermelon). Percent infection of plants was measured through symptom observation on the test plants and the presence of the virus was confirmed through an enzyme-linked immunosorbent assay with appropriate antibodies. Statistical analysis was performed using one-way ANOVA based on data collected from three independent experiments.
Through comparative analysis of percent infection of test plants, a similar trend of efficacy among 16 disinfectants was observed between the two pathosystems. Four common disinfectants with broad spectrum activities against two different tobamoviruses were identified. Those effective disinfectants with 90-100% efficacy against both tobamoviruses were 0.5% Lactoferrin, 2% Virocid, and 10% Clorox, plus 2% Virkon against CGMMV and 3% Virkon against ToBRFV. In addition, SP2700 generated a significant effect against CGMMV, but poorly against ToBRFV.
Identification of common disinfectants against ToBRFV and CGMMV, two emerging tobamoviruses in two different pathosystems suggest their potential broader effects against other tobamoviruses or even other viruses.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In nanocellular foam production, achieving cell sizes less than 100 nm with low relative densities is challenging. In this study, poly (methyl methacrylate) (PMMA) was blended with three ...thermoplastic polyurethanes (TPUs) of different hardnesses to study the impact of TPUs on the nanocellular structure and foam density. The viscosity of TPU controlled the nanostructure of the blend. Blending 2 wt% TPU with PMMA generated a well-dispersed system, with the smallest TPU particle size less than 100 nm. The CO2-blown nanocellular foam possessed a bouquet-like structure with a cell density of 1016 cells/cm3. These TPU nanoparticles provided an ultrahigh nucleation efficiency of 3674 times. The unexpected increase in nucleation efficiency could be due to the well-dispersed TPU particles. Such a high nucleation efficiency created an open-cell structure with decreased strut fraction and significantly lowered the foam density. We can create a nanocellular foam with a relative density of less than 0.2 and an average cell size of less than 100. Adding 2 wt% of TPU to PMMA reduces the relative density by 32.26%, from 0.31 to 0.18.
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•Blending TPU and PMMA generated a well-dispersed system of nanosized particles.•A bouquet-like nanocellular structure with a high cell density was observed.•Liquid-liquid nucleation happened at the PMMA-TPU interfaces.•TPU nanoparticles provided an ultrahigh nucleation efficiency of 3674 times.•A relative density of 0.18 with a cell size of less than 100 nm was obtained.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The use of social media has accelerated information sharing and instantaneous communications. The low barrier to enter social media enables more users to participate and makes them stay engaged ...longer, while incentivizing individuals with a hidden agenda to use disinformation to manipulate information and influence opinions. Disinformation, such as fake news, hoaxes, and conspiracy theories, has increasingly been weaponized to divide people and create detrimental societal effects. Therefore, it is imperative to understand disinformation and systematically investigate how we can improve resistance against it, taking into account the tension between the need for information and the need for security and protection against disinformation. In this survey, we look into the concepts, methods, and recent advancements of detecting disinformation from a computational perspective. We will also discuss open issues and future research directions for combating disinformation on social media.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Summary
Bottle gourd (Lagenaria siceraria (Mol.) Strandl.) is an economically important vegetable crop and one of the earliest domesticated crops. However, the population history and genomic ...diversification of bottle gourd have not been extensively studied.
We generated a comprehensive bottle gourd genome variation map from genome sequences of 197 world‐wide representative accessions, which enables a genome‐wide association study for identifying genomic loci associated with resistance to zucchini yellow mosaic virus, and constructed a bottle gourd pangenome that harbors 1534 protein‐coding genes absent in the reference genome.
Demographic analyses uncover that domesticated bottle gourd originated in Southern Africa c. 12 000 yr ago, and subsequently radiated to the New World via the Atlantic drift and to Eurasia through the efforts of early farmers in the initial Holocene. The identified highly differentiated genomic regions among different bottle gourd populations harbor many genes contributing to their local adaptations such as those related to disease resistance and stress tolerance. Presence/absence variation analysis of genes in the pangenome reveals numerous genes including those involved in abiotic/biotic stress responses that have been under selection during the world‐wide expansion of bottle gourds.
The bottle gourd variation map and pangenome provide valuable resources for future functional studies and genomics‐assisted breeding.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Summary
Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and ...genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.
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BFBNIB, DOBA, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UILJ, UKNU, UL, UM, UPUK
The phytohormones abscisic acid (ABA) and gibberellin (GA) antagonistically mediate diverse plant developmental processes including seed dormancy and germination, root development, and flowering time ...control, and thus the optimal balance between ABA and GA is essential for plant growth and development. Although more than a half and one century have passed since the initial discoveries of ABA and GA, respectively, the precise mechanisms underlying ABA–GA antagonism still need further investigation. Emerging evidence indicates that two APETALA 2 (AP2)-domain-containing transcription factors (ATFs), ABI4 in Arabidopsis and OsAP2-39 in rice, play key roles in ABA and GA antagonism. These two transcription factors precisely regulate the transcription pattern of ABA and GA biosynthesis or inactivation genes, mediating ABA and GA levels. In this Viewpoint article, we try to shed light on the effects of ATFs on ABA–GA antagonism, and summarize the overlapping but distinct biological functions of these ATFs in the antagonism between ABA and GA. Finally, we strongly propose that further research is needed into the detailed roles of additional numerous ATFs in ABA and GA crosstalk, which will improve our understanding of the antagonism between these two phytohormones.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
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