Coevolution of relationship and interaction in cooperative dynamical multiplex networks.

While actors in a population can interact with anyone else freely, social relations significantly influence our inclination toward particular individuals. The consequence of such interactions, however, may also form the intensity of our relations established earlier. These dynamical processes are captured via a coevolutionary model staged in multiplex networks with two distinct layers. In a so-called relationship layer, the weights of edges among players may change in time as a consequence of games played in the alternative interaction layer. As an reasonable assumption, bilateral cooperation confirms while mutual defection weakens these weight factors. Importantly, the fitness of a player, which basically determines the success of a strategy imitation, depends not only on the payoff collected from interactions, but also on the individual relationship index calculated from the mentioned weight factors of related edges. Within the framework of weak prisoner's dilemma situation, we explore the potential outcomes of the mentioned coevolutionary process where we assume different topologies for relationship layer. We find that higher average degree of the relationship graph is more beneficial to maintain cooperation in regular graphs, but the randomness of links could be a decisive factor in harsh situations. Surprisingly, a stronger coupling between relationship index and fitness discourage the evolution of cooperation by weakening the direct consequence of a strategy change. To complete our study, we also monitor how the distribution of relationship index vary and detect a strong relation between its polarization and the general cooperation level.

Inhibition and activation of interactions in networked weak prisoner's dilemma.

In the framework of the coevolution dynamics of the weak prisoner's dilemma, inspired by prior empirical research, we present a coevolutionary model with local network dynamics in a static network framework. Viewing the edges of the network as social interactions between individuals, when individuals play the weak prisoner's dilemma game, they accumulate both payoffs and social interaction willingness based on a payoff matrix of the social interaction willingness we constructed. The edges are then inhibiting or activating based on the social interaction willingness of the two individuals, and individuals only interact with others through activated edges, resulting in local network dynamics in a static network framework. Individuals who receive more cooperation will be more likely to activate the edges around them, meaning they will participate in more social interactions. Conversely, individuals who receive more defects will do the opposite. Specifically, we investigate the evolutionary dynamics of cooperation under different levels of sensitivity to social interaction willingness and the temptation to defect. Through the simulation, we find that sparse cooperator clusters can expand greatly when social interaction sensitivity and temptation to defect are low. In contrast, dense cooperator clusters form rapidly in a high social interaction sensitivity, which protects the cooperation from high temptation.

A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance.

The lemon (Citrus limon; family Rutaceae) is one of the most important and popular fruits worldwide. Lemon also tolerates huanglongbing (HLB) disease, which is a devastating citrus disease. Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing, Oxford Nanopore 50-kb ultra-long, and high-throughput chromatin conformation capture technologies. The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps, while a total of 633.0 Mb genomic sequences were generated. The origination analysis identified 338.5 Mb genomic sequences originating from citron (53.5%), 147.4 Mb from mandarin (23.3%), and 147.1 Mb from pummelo (23.2%). The genome included 30 528 protein-coding genes, and most of the assembled sequences were found to be repetitive sequences. Several significantly expanded gene families were associated with plant-pathogen interactions, plant hormone signal transduction, and the biosynthesis of major active components, such as terpenoids and flavor compounds. Most HLB-tolerant genes were expanded in the lemon genome, such as 2-oxoglutarate (2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1, cell wall-related genes, and lignin synthesis genes. Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon. Our results provide insight into lemon genome evolution, active component biosynthesis, and genes associated with HLB tolerance.

Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus.

Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B. Here, we presented three C. paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids. Resequencing analysis of 45 C. paliurus individuals uncovered two bottlenecks, consistent with the known events of environmental changes, and many selectively swept genes involved in critical biological functions, including plant defense and secondary metabolite biosynthesis. We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes, in particular gibberellin-related genes, associated with the heterodichogamy in C. paliurus species. Our study sheds light on evolutionary history of C. paliurus and provides genomic resources to study the medicinal herbs.

Spatial evolution of cooperation with variable payoffs.

In the evolution of cooperation, the individuals' payoffs are commonly random in real situations, e.g., the social networks and the economic regions, leading to unpredictable factors. Therefore, there are chances for each individual to obtain the exceeding payoff and risks to get the low payoff. In this paper, we consider that each individual's payoff follows a specific probability distribution with a fixed expectation, where the normal distribution and the exponential distribution are employed in our model. In the simulations, we perform the models on the weak prisoner's dilemmas (WPDs) and the snowdrift games (SDGs), and four types of networks, including the hexagon lattice, the square lattice, the small-world network, and the triangular lattice are considered. For the individuals' normally distributed payoff, we find that the higher standard deviation usually inhibits the cooperation for the WPDs but promotes the cooperation for the SDGs. Besides, with a higher standard deviation, the cooperation clusters are usually split for the WPDs but constructed for the SDGs. For the individuals' exponentially distributed payoff, we find that the small-world network provides the best condition for the emergence of cooperators in WPDs and SDGs. However, when playing SDGs, the small-world network allows the smallest space for the pure cooperative state while the hexagon lattice allows the largest.

Evolutionary multigame with conformists and profiteers based on dynamic complex networks.

Evolutionary game on complex networks provides a new research framework for analyzing and predicting group decision-making behavior in an interactive environment, in which most researchers assumed players as profiteers. However, current studies have shown that players are sometimes conformists rather than profit-seeking in society, but most research has been discussed on a simple game without considering the impact of multiple games. In this paper, we study the influence of conformists and profiteers on the evolution of cooperation in multiple games and illustrate two different strategy-updating rules based on these conformists and profiteers. Different from previous studies, we introduce a similarity between players into strategy-updating rules and explore the evolutionary game process, including the strategy updating, the transformation of players' type, and the dynamic evolution of the network structure. In the simulation, we implement our model on scale-free and regular networks and provide some explanations from the perspective of strategy transition, type transition, and network topology properties to prove the validity of our model.

Dynamic changes of IgM and IgG antibodies in asymptomatic patients as an effective way to detect SARS-CoV-2 infection.

BACKGROUND: COVID-19 has become a global pandemic, and close contacts and asymptomatic patients are worthy of attention. METHODS: A total of 1844 people in close contacts with 76 COVID-19 patients were investigated, and nasopharyngeal swabs and venous blood were collected for centralized medical quarantine observation. Real-time fluorescence was used to detect SARS-CoV-2 nucleic acid in nasopharyngeal swabs of all close contacts, and the colloidal gold method was used to detect serum-specific antibodies. Levels of IgM- and IgG-specific antibodies were detected quantitatively through chemiluminescence from the first nucleic acid turned negative date (0 week) and on weekly intervals of ≤1 week, 1-2 weeks, 2-3 weeks, 3-4 weeks, 4-5 weeks, 5-6 weeks, and 6-7 weeks. RESULTS: The total positive rate of the colloidal gold method (88.5%, 23/26) was significantly higher (χ2  = 59.182, p < 0.001) than that of the healthy control group (2.0%, 1/50). There was significant difference in IgG concentration at different time points (0-7 weeks) after negative nucleic acid conversion (χ2  = 14.034, p = 0.029). Serum IgG levels were significantly higher at weekly time points of 4-5 weeks (Z = -2.399, p = 0.016), 5-6 weeks (Z = -2.049, p = 0.040), and 6-7 weeks (Z = -2.197, p = 0.028) compared with 1-2 weeks after negative nucleic acid conversion. However, there was no significant difference (χ2  = 4.936, p = 0.552) in IgM concentration between time points tested (0-7 weeks) after negative nucleic acid conversion. The positive rates of IgM and IgG in asymptomatic patients (χ2  = 84.660, p < 0.001) were significantly higher than those in the healthy control group (χ2  = 9.201, p = 0.002) within 7 weeks of negative nucleic acid conversion. CONCLUSIONS: The IgG concentration in asymptomatic cases remained at a high level after nucleic acid turned negative. Nucleic acid detection combined with IgM and IgG antibody detection is an effective way to screen asymptomatic infections.

Matrix metalloproteinase 3 as a valuable marker for patients with COVID-19.

The situation of the coronavirus disease 2019 (COVID-19) continues to evolve, our study explored the significance of serum levels of matrix metalloproteinase 3 (MMP3) as a marker for patients with COVID-19. Sixty-two COVID-19 patients in the First Hospital of Hunan University of Chinese Medicine and Loudi Center for Diseases Prevention and Control, from January to March 2020, were sampled as the novel coronavirus pneumonia infected group. One hundred and thirty-one cases from the First Hospital of Hunan University of Chinese Medicine, including 67 healthy individuals and 64 non-COVID-19 inpatients, served as the noninfected group. Approximately every 5 days, sera from 20 cases were collected and analyzed three times, using an automatic biochemical analyzer, to detect serum MMP3 concentrations. Correlation was analyzed between MMP3 and other proinflammatory cytokines. Following normality tests, differences in serum MMP3 levels between the infected and noninfected group were analyzed via SPSS (version 25.0) software, using the Wilcoxon rank sum test. The MMP3 concentration was 44.44 (23.46 ~ 72.12) ng/mL in the infected group and 32.42 (28.16 ~ 41.21) ng/mL in the noninfected group. The difference between the two groups was statistically significant (Z = -2.799, P = .005 < .05). A positive correlation was found between MMP3 and interleukin 1ß (IL-1ß; r = .681, P = .000 < .05), and IL-6 (r = .529, P = .002 < .05). Serum MMP3 concentration, measured over three separate time points, were 55.98 (30.80 ~ 75.97) ng/mL, 34.84 (0.00 ~ 51.84) ng/mL, and 5.71 (0.00 ~ 40.46) ng/mL, respectively. Detection of serum MMP3 levels may play an important role in the development of therapeutic approaches for COVID-19 and may indicate the severity of disease.

Shape selective plate-form Ga(2)O(3) with strong metal-support interaction to overlying Pd for hydrogenation of CO(2) to CH(3)OH.

A stronger metal-support interaction between Pd and plate-form Ga(2)O(3) nanocrystals covered with the predominant 002 surface than other Ga(2)O(3) surfaces is found, which gives higher methanol yield in catalytic CO(2) hydrogenation.