Particle swarm optimization (PSO) relies on its learning strategy to guide its search direction. Traditionally, each particle utilizes its historical best experience and its neighborhood's best ...experience through linear summation. Such a learning strategy is easy to use, but is inefficient when searching in complex problem spaces. Hence, designing learning strategies that can utilize previous search information (experience) more efficiently has become one of the most salient and active PSO research topics. In this paper, we proposes an orthogonal learning (OL) strategy for PSO to discover more useful information that lies in the above two experiences via orthogonal experimental design. We name this PSO as orthogonal learning particle swarm optimization (OLPSO). The OL strategy can guide particles to fly in better directions by constructing a much promising and efficient exemplar. The OL strategy can be applied to PSO with any topological structure. In this paper, it is applied to both global and local versions of PSO, yielding the OLPSO-G and OLPSO-L algorithms, respectively. This new learning strategy and the new algorithms are tested on a set of 16 benchmark functions, and are compared with other PSO algorithms and some state of the art evolutionary algorithms. The experimental results illustrate the effectiveness and efficiency of the proposed learning strategy and algorithms. The comparisons show that OLPSO significantly improves the performance of PSO, offering faster global convergence, higher solution quality, and stronger robustness.
Social learning in particle swarm optimization (PSO) helps collective efficiency, whereas individual reproduction in genetic algorithm (GA) facilitates global effectiveness. This observation recently ...leads to hybridizing PSO with GA for performance enhancement. However, existing work uses a mechanistic parallel superposition and research has shown that construction of superior exemplars in PSO is more effective. Hence, this paper first develops a new framework so as to organically hybridize PSO with another optimization technique for "learning." This leads to a generalized "learning PSO" paradigm, the *L-PSO. The paradigm is composed of two cascading layers, the first for exemplar generation and the second for particle updates as per a normal PSO algorithm. Using genetic evolution to breed promising exemplars for PSO, a specific novel *L-PSO algorithm is proposed in the paper, termed genetic learning PSO (GL-PSO). In particular, genetic operators are used to generate exemplars from which particles learn and, in turn, historical search information of particles provides guidance to the evolution of the exemplars. By performing crossover, mutation, and selection on the historical information of particles, the constructed exemplars are not only well diversified, but also high qualified. Under such guidance, the global search ability and search efficiency of PSO are both enhanced. The proposed GL-PSO is tested on 42 benchmark functions widely adopted in the literature. Experimental results verify the effectiveness, efficiency, robustness, and scalability of the GL-PSO.
Summary
Nitrogen (N) is one of the key essential macronutrients that affects rice growth and yield. Inorganic N fertilizers are excessively used to boost yield and generate serious collateral ...environmental pollution. Therefore, improving crop N use efficiency (NUE) is highly desirable and has been a major endeavour in crop improvement. However, only a few regulators have been identified that can be used to improve NUE in rice to date. Here we show that the rice NIN‐like protein 4 (OsNLP4) significantly improves the rice NUE and yield. Field trials consistently showed that loss‐of‐OsNLP4 dramatically reduced yield and NUE compared with wild type under different N regimes. In contrast, the OsNLP4 overexpression lines remarkably increased yield by 30% and NUE by 47% under moderate N level compared with wild type. Transcriptomic analyses revealed that OsNLP4 orchestrates the expression of a majority of known N uptake, assimilation and signalling genes by directly binding to the nitrate‐responsive cis‐element in their promoters to regulate their expression. Moreover, overexpression of OsNLP4 can recover the phenotype of Arabidopsis nlp7 mutant and enhance its biomass. Our results demonstrate that OsNLP4 plays a pivotal role in rice NUE and sheds light on crop NUE improvement.
In nature, almost every organism ages and has a limited lifespan. Aging has been explored by biologists to be an important mechanism for maintaining diversity. In a social animal colony, aging makes ...the old leader of the colony become weak, providing opportunities for the other individuals to challenge the leadership position. Inspired by this natural phenomenon, this paper transplants the aging mechanism to particle swarm optimization (PSO) and proposes a PSO with an aging leader and challengers (ALC-PSO). ALC-PSO is designed to overcome the problem of premature convergence without significantly impairing the fast-converging feature of PSO. It is characterized by assigning the leader of the swarm with a growing age and a lifespan, and allowing the other individuals to challenge the leadership when the leader becomes aged. The lifespan of the leader is adaptively tuned according to the leader's leading power. If a leader shows strong leading power, it lives longer to attract the swarm toward better positions. Otherwise, if a leader fails to improve the swarm and gets old, new particles emerge to challenge and claim the leadership, which brings in diversity. In this way, the concept "aging" in ALC-PSO actually serves as a challenging mechanism for promoting a suitable leader to lead the swarm. The algorithm is experimentally validated on 17 benchmark functions. Its high performance is confirmed by comparing with eight popular PSO variants.
Background and purpose
Recent genetic progress has shown many causative/risk genes linked to Parkinson's disease (PD), mainly in patients of European ancestry. The study aimed to investigate the ...PD‐related genes and determine the mutational spectrum of early‐onset PD in ethnic Chinese.
Methods
In this study, whole‐exome sequencing and/or gene dosage analysis were performed in 704 early‐onset PD (EOPD) patients (onset age ≤45 years) and 1866 controls. Twenty‐six PD‐related genes and 20 other genes linked to neurodegenerative and lysosome diseases were analysed.
Results
Eighty‐two (11.6%, 82/704) EOPD patients carrying rare pathogenic/likely pathogenic variants in PD‐related genes were identified. The mutation frequency in autosomal recessive inheritance EOPD (42.9%, 27/63) was much higher than that in autosomal dominant inheritance EOPD (0.9%, 12/110) or sporadic EOPD (8.1%, 43/531). Bi‐allelic mutations in PRKN were the most frequent, accounting for 5.1% of EOPD cases. Three common pathogenic variants, p.A53V in SNCA, p.G284R in PRKN and p.P53Afs*38 in CHCHD2, occur exclusively in Asians. The putative damaging variants from GBA, PRKN, DJ1, PLA2G6 and GCH1 contributed to the collective risk for EOPD. Notably, the protein‐truncating variants in CHCHD2 were enriched in EOPD, especially for p.P53Afs*38, which was also found in three patients from an independent cohort of patients with late‐onset PD (n = 1300). Functional experiments confirmed that truncated CHCHD2 variants cause loss of function and are linked to mitochondrial dysfunction.
Conclusions
Our study reveals that the genetic spectrum of EOPD in Chinese, which may help develop genetic scanning strategies, provided more evidence supporting CHCHD2 in PD.
Three common pathogenic variants, p.A53V in SNCA, p.G284R in PRKN and p.P53Afs*38 in CHCHD2, occur exclusively in Asians. The putative damaging variants from GBA, PRKN, DJ1 and PLA2G6 contributed the collective risk for early‐onset Parkinson’s disease (PD). The protein‐truncating variants in CHCHD2 were significantly enriched in early‐onset PD, especially for p.P53Afs*38, which was confirmed in an independent cohort of patients with late‐onset PD and functional experiments.
Nitrogen (N) is an essential macronutrient for crop growth and yield. Improving the N use efficiency (NUE) of crops is important to agriculture. However, the molecular mechanisms underlying NUE ...regulation remain largely elusive. Here we report that the OsNLP3 (NIN‐like protein 3) regulates NUE and grain yield in rice under N sufficient conditions. OsNLP3 transcript level is significantly induced by N starvation and its protein nucleocytosolic shuttling is specifically regulated by nitrate. Loss‐of‐function of OsNLP3 reduces plant growth, grain yield, and NUE under sufficient nitrate conditions, whereas under low nitrate or different ammonium conditions, osnlp3 mutants show no clear difference from the wild type. Importantly, under sufficient N conditions in the field, OsNLP3 overexpression lines display improved grain yield and NUE compared with the wild type. OsNLP3 orchestrates the expression of multiple N uptake and assimilation genes by directly binding to the nitrate‐responsive cis‐elements in their promoters. Overall, our study demonstrates that OsNLP3, together with OsNLP1 and OsNLP4, plays overlapping and differential roles in N acquisition and NUE, and modulates NUE and the grain yield increase promoted by N fertilizer. Therefore, OsNLP3 is a promising candidate gene for the genetic improvement of grain yield and NUE in rice.
Summary Statement
Crop nitrogen use efficiency (NUE) is an important agronomic trait. But the molecular mechanisms underlying NUE regulation are not well understood. This study reveals that rice NIN‐like protein 3 (OsNLP3) regulates NUE and grain yield especially under N sufficient conditions and is a promising candidate gene for improving grain yield and NUE in rice.
Nitrogen is essential for plant survival and growth. Excessive application of nitrogenous fertilizer has generated serious environment pollution and increased production cost in agriculture. To deal ...with this problem, tremendous efforts have been invested worldwide to increase the nitrogen use ability of crops. However, only limited success has been achieved to date. Here we report that NLP7 (NIN-LIKE PROTEIN 7) is a potential candidate to improve plant nitrogen use ability. When overexpressed in Arabidopsis, NLP7 increases plant biomass under both nitrogen-poor and -rich conditions with better-developed root system and reduced shoot/root ratio. NLP7-overexpressing plants show a significant increase in key nitrogen metabolites, nitrogen uptake, total nitrogen content, and expression levels of genes involved in nitrogen assimilation and signalling. More importantly, overexpression of NLP7 also enhances photosynthesis rate and carbon assimilation, whereas knockout of NLP7 impaired both nitrogen and carbon assimilation. In addition, NLP7 improves plant growth and nitrogen use in transgenic tobacco (Nicotiana tabacum). Our results demonstrate that NLP7 significantly improves plant growth under both nitrogen-poor and -rich conditions by coordinately enhancing nitrogen and carbon assimilation and sheds light on crop improvement.
ASFV is a large DNA virus that is highly pathogenic in domestic pigs. How this virus is sensed by the innate immune system as well as why it is so virulent remains enigmatic. In this study, we show ...that the ASFV genome contains AT-rich regions that are recognized by the DNA-directed RNA polymerase III (Pol-III), leading to viral RNA sensor RIG-I-mediated innate immune responses. We further show that ASFV protein I267L inhibits RNA Pol-III-RIG-I-mediated innate antiviral responses. I267L interacts with the E3 ubiquitin ligase Riplet, disrupts Riplet-RIG-I interaction and impairs Riplet-mediated K63-polyubiquitination and activation of RIG-I. I267L-deficient ASFV induces higher levels of interferon-β, and displays compromised replication both in primary macrophages and pigs compared with wild-type ASFV. Furthermore, I267L-deficiency attenuates the virulence and pathogenesis of ASFV in pigs. These findings suggest that ASFV I267L is an important virulence factor by impairing innate immune responses mediated by the RNA Pol-III-RIG-I axis.
A highly enantioselective 3+2 annulation of isatin-derived Morita-Baylis-Hillman (MBH) carbonates and 3-nitroindoles was enabled by a chiral DMAP-thiourea bifunctional catalyst, affording the ...corresponding polycyclic spirooxindoles bearing three consecutive stereocenters with good to excellent yields and enantioselectivities. Transformations of the annulation product were subsequently elaborated and the preliminary biological assays demonstrated that these artificial spirooxindoles potentially inhibited pancreatic lipase in a dose-dependent manner.
A large number of new causative and risk genes for amyotrophic lateral sclerosis (ALS) have been identified mostly in patients of European ancestry. In contrast, we know relatively little regarding ...the genetics of ALS in other ethnic populations. This study aims to provide a comprehensive analysis of the genetics of ALS in an unprecedented large cohort of Chinese mainland population and correlate with the clinical features of rare variants carriers.
A total of 1587 patients, including 64 familial ALS (FALS) and 1523 sporadic ALS (SALS), and 1866 in-house controls were analysed by whole-exome sequencing and/or testing for G4C2 repeats in
. Forty-one ALS-associated genes were analysed.
155 patients, including 26 (40.6%) FALS and 129 (8.5%) SALS, carrying rare pathogenic/likely pathogenic (P/LP) variants of ALS causative genes were identified.
was the most common mutated gene, followed by
,
,
,
and
. By burden analysis, rare variants in
,
and
contributed to the collective risk for ALS (p<2.5e-6) at the gene level, but at the allelic level
p.Gly294Val and
p.Arg521Cys and p.Arg521His were the most important single variants causing ALS. Clinically, P/LP variants in
and
were associated with poor prognosis, in
linked with younger age of onset, and
repeats tended to affect cognition.
Our data provide essential information for understanding the genetic and clinical features of ALS in China and for optimal design of genetic testing and evaluation of disease prognosis.
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