Data_Sheet_3_Componential usage patterns in dengue 4 viruses reveal their better evolutionary adaptation to humans.doc

There have been at least four types of dengue outbreaks in the past few years. The evolutionary characteristics of dengue viruses have aroused great concerns. The evolutionary characteristics of dengue 4 viruses are studied in the present study based on their base usage patterns and codon usage patterns. The effective number of codons and relative synonymous codon usage (RSCU) values of four types of dengue viruses were counted or calculated. The Kullback–Leibler (K–L) divergences of relative synonymous codon usage from dengue viruses to humans and the Kullback–Leibler divergences of amino acid usage patterns from dengue viruses to humans were calculated to explore the adaptation levels of dengue viruses. The results suggested that: (1) codon adaptation in dengue 4 viruses occurred through an evolutionary process from 1956 to 2021, (2) overall relative synonymous codon usage values of dengue 4 viruses showed more similarities to humans than those of other subtypes of dengue viruses, and (3) the smaller Kullback–Leibler divergence of amino acid usage and relative synonymous codon usage from dengue viruses to humans indicated that the dengue 4 viruses adapted to human hosts better. All results indicated that both mutation pressure and natural selection pressure contributed to the codon usage pattern of dengue 4 viruses more obvious than to other subtypes of dengue viruses and that the dengue 4 viruses adapted to human hosts better than other types of dengue viruses during their evolutionary process.</p

Data_Sheet_2_Componential usage patterns in dengue 4 viruses reveal their better evolutionary adaptation to humans.xls

There have been at least four types of dengue outbreaks in the past few years. The evolutionary characteristics of dengue viruses have aroused great concerns. The evolutionary characteristics of dengue 4 viruses are studied in the present study based on their base usage patterns and codon usage patterns. The effective number of codons and relative synonymous codon usage (RSCU) values of four types of dengue viruses were counted or calculated. The Kullback–Leibler (K–L) divergences of relative synonymous codon usage from dengue viruses to humans and the Kullback–Leibler divergences of amino acid usage patterns from dengue viruses to humans were calculated to explore the adaptation levels of dengue viruses. The results suggested that: (1) codon adaptation in dengue 4 viruses occurred through an evolutionary process from 1956 to 2021, (2) overall relative synonymous codon usage values of dengue 4 viruses showed more similarities to humans than those of other subtypes of dengue viruses, and (3) the smaller Kullback–Leibler divergence of amino acid usage and relative synonymous codon usage from dengue viruses to humans indicated that the dengue 4 viruses adapted to human hosts better. All results indicated that both mutation pressure and natural selection pressure contributed to the codon usage pattern of dengue 4 viruses more obvious than to other subtypes of dengue viruses and that the dengue 4 viruses adapted to human hosts better than other types of dengue viruses during their evolutionary process.</p

Data_Sheet_1_Componential usage patterns in dengue 4 viruses reveal their better evolutionary adaptation to humans.xls

There have been at least four types of dengue outbreaks in the past few years. The evolutionary characteristics of dengue viruses have aroused great concerns. The evolutionary characteristics of dengue 4 viruses are studied in the present study based on their base usage patterns and codon usage patterns. The effective number of codons and relative synonymous codon usage (RSCU) values of four types of dengue viruses were counted or calculated. The Kullback–Leibler (K–L) divergences of relative synonymous codon usage from dengue viruses to humans and the Kullback–Leibler divergences of amino acid usage patterns from dengue viruses to humans were calculated to explore the adaptation levels of dengue viruses. The results suggested that: (1) codon adaptation in dengue 4 viruses occurred through an evolutionary process from 1956 to 2021, (2) overall relative synonymous codon usage values of dengue 4 viruses showed more similarities to humans than those of other subtypes of dengue viruses, and (3) the smaller Kullback–Leibler divergence of amino acid usage and relative synonymous codon usage from dengue viruses to humans indicated that the dengue 4 viruses adapted to human hosts better. All results indicated that both mutation pressure and natural selection pressure contributed to the codon usage pattern of dengue 4 viruses more obvious than to other subtypes of dengue viruses and that the dengue 4 viruses adapted to human hosts better than other types of dengue viruses during their evolutionary process.</p

Convergence faible de la statistique lineaire de rang pour des variables aleatoires faiblement dependantes et non stationnaires

SIGLECNRS T Bordereau / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Incorporating Polarization and Charge Transfer into a Point-Charge Model for Water Using Machine Learning

Rigid nonpolarizable water models with fixed point charges have been widely employed in molecular dynamics simulations due to their efficiency and reasonable accuracy for the potential energy surface. However, the dipole moment surface of water is not necessarily well-described by the same fixed charges, leading to failure in reproducing dipole-related properties. Here, we developed a machine-learning model trained against electronic structure data to assign point charges for water, and the resulting dipole moment surface significantly improved the predictions of the dielectric constant and the low-frequency IR spectrum of liquid water. Our analysis reveals that within our atom-centered point-charge description of the dipole moment surface, the intermolecular charge transfer is the major source of the peak intensity at 200 cm–1, whereas the intramolecular polarization controls the enhancement of the dielectric constant. The effects of exact Hartree–Fock exchange in the hybrid density functional on these properties are also discussed

Aggregation Kinetics of Hematite Particles in the Presence of Outer Membrane Cytochrome OmcA of <i>Shewanella oneidenesis</i> MR‑1

The aggregation behavior of 9, 36, and 112 nm hematite particles was studied in the presence of OmcA, a bacterial extracellular protein, in aqueous dispersions at pH 5.7 through time-resolved dynamic light scattering, electrophoretic mobility, and circular dichroism spectra, respectively. At low salt concentration, the attachment efficiencies of hematite particles in all sizes first increased, then decreased, and finally remained stable with the increase of OmcA concentration, indicating the dominant interparticle interaction changed along with the increase in the protein-to-particle ratio. Nevertheless, at high salt concentration, the attachment efficiencies of all hematite samples gradually decreased with increasing OmcA concentration, which can be attributed to increasing steric force. Additionally, the aggregation behavior of OmcA–hematite conjugates was more correlated to total particle–surface area than primary particle size. It was further established that OmcA could stabilize hematite nanoparticles more efficiently than bovine serum albumin (BSA), a model plasma protein, due to the higher affinity of OmcA to hematite surface. This study highlighted the effects of particle properties, solution conditions, and protein properties on the complicated aggregation behavior of protein–nanoparticle conjugates in aqueous environments

Different Stages, Different Signals: The Modulating Effect of Cognitive Conflict on Subsequent Processing

<div><p>The present study used event-related potentials (ERPs) to investigate the function of signals induced by cognitive conflict during the detection stage and the resolution stage of perceptual processing. The study used a combination of the Stroop task and an affective priming task to examine the conflict priming effect when the stimulus onset asynchrony (SOA) was 200 ms or 800 ms. Behavioral results showed that the RTs were shorter for positive targets following congruent primes relative to incongruent primes, and for negative targets following incongruent primes relative to congruent primes when the SOA was 200 ms. ERP results showed that the N2 amplitudes (200–300 ms) for incongruent stimuli were significantly larger than for congruent stimuli in the Stroop task, which indicated a significant conflict effect. Moreover, the N400 amplitudes (500–700 ms) for positive targets after congruent primes were significantly lower than those after incongruent primes when the SOA was 200 ms, which showed a significant negative priming effect. While the SOA was 800 ms, behavioral results showed that the RTs were shorter for positive targets following incongruent primes relative to congruent primes. ERP results showed that the N2 amplitudes (200–300 ms) for incongruent stimuli were significantly larger than for congruent stimuli in the Stroop task, which indicated a significant conflict effect. The N400 amplitudes (1100–1300 ms) for the negative targets after congruent primes were significantly lower than those after incongruent primes when the SOA was 800 ms, which showed a significant positive priming effect. The results demonstrated that the functions of signals induced by cognitive conflict were reversed in two different cognitive processing stages.</p></div

Rational Design of Hierarchical Nanotubes through Encapsulating CoSe₂ Nanoparticles into MoSe₂/C Composite Shells with Enhanced Lithium and Sodium Storage Performance

Transition-metal diselenides have been extensively studied as desirable anode candidates for both lithium-ion batteries (LIBs) and sodium-ion batteries (SIBs) because of their high theoretical capacities. However, it is of great challenge to achieve satisfactory cycling performance, especially for larger sodium ion storage, originated from electrode deterioration upon large volume change. Herein, we reported the construction of hierarchical tubular hybrid nanostructures through encapsulating CoSe₂ nanoparticles into MoSe₂/C composite shells via a simple two-step strategy including a hydrothermal method followed by vapor-phase selenization process. The unique tubular structure enables the highly reversible Li/Na storage with high specific capacity, enhanced cycling stability, and superior rate performance. It is indicated that the contribution of partial pseudocapacitive behavior greatly improves the rate capability for SIBs, where a high capacity retention of 81.5% can be obtained when the current densities range from 0.1 to 3 A g^–1 (460 mA h g^–1 at 0.1 A g^–1 vs 379 mA h g^–1 at 3 A g^–1). This work provides an effective design rationale on transition-metal diselenide-based tubular nanostructures as superior hosts for both Li and Na ions, which could push forward the development of practical applications of transition-metal diselenide-based anodes in LIBs and SIBs

The average ERPs at Cz and CPz for CP (congruent—positive), CN (congruent—negative), IP (incongruent—positive) and IN (incongruent—negative) conditions in priming effect (SOA = 800ms).

<p>Red line refers to positive target after congruent prime condition; red dashed line refers to negative target after congruent prime condition; black line refers to positive target after incongruent prime condition and black dashed line refers to negative target after incongruent prime condition.</p

The average ERPs at Cz and FCz for congruent prime and incongruent prime conditions in Stroop effect (SOA = 800ms).

<p>Red line represents incongruent prime condition and black line represents congruent prime condition.</p