Smooth curve of evolutionary rate: a psychological and mathematical artifact

AbstractWe identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.

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Experimental Validation on Intersection Turning Trajectory Prediction Method for Advanced Driver Assistance System Based on Triclothoidal Curve

Applied Sciences ◽

10.3390/app11135900 ◽

2021 ◽

Vol 11 (13) ◽

pp. 5900

Author(s):

Yohei Fujinami ◽

Pongsathorn Raksincharoensak ◽

Shunsaku Arita ◽

Rei Kato

Keyword(s):

Traffic Accidents ◽

Computational Cost ◽

Prediction Method ◽

Smooth Curve ◽

Assistance System ◽

Driver Assistance ◽

Driver Assistance Systems ◽

Trajectory Prediction ◽

Left Turn ◽

Left Hand

Advanced driver assistance systems (ADAS) for crash avoidance, when making a right-turn in left-hand traffic or left-turn in right-hand traffic, are expected to further reduce the number of traffic accidents caused by automobiles. Accurate future trajectory prediction of an ego vehicle for risk prediction is important to activate the assistance system correctly. Our objectives are to propose a trajectory prediction method for ADAS for safe intersection turnings and to evaluate the effectiveness of the proposed prediction method. Our proposed curve generation method is capable of generating a smooth curve without discontinuities in the curvature. By incorporating the curve generation method into the vehicle trajectory prediction, the proposed method could simulate the actual driving path of human drivers at a low computational cost. The curve would be required to define positions, angles, and curvatures at its initial and terminal points. Driving experiments conducted at real city traffic intersections proved that the proposed method could predict the trajectory with a high degree of accuracy for various shapes and sizes of the intersections. This paper also describes a method to determine the terminal conditions of the curve generation method from intersection features. We set a hypothesis where the conditions can be defined individually from intersection geometry. From the hypothesis, a formula to determine the parameter was derived empirically from the driving experiments. Public road driving experiments indicated that the parameters for the trajectory prediction could be appropriately estimated by the obtained empirical formula.

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Higher rank Clifford indices of curves on a K3 surface

Selecta Mathematica ◽

10.1007/s00029-021-00664-z ◽

2021 ◽

Vol 27 (3) ◽

Author(s):

Soheyla Feyzbakhsh ◽

Chunyi Li

Keyword(s):

Vector Bundles ◽

Plane Curve ◽

Smooth Curve ◽

Line Bundles ◽

K3 Surface ◽

Clifford Index ◽

Smooth Plane ◽

Higher Rank ◽

Rank Vector ◽

Semistable Vector Bundle

AbstractLet (X, H) be a polarized K3 surface with $$\mathrm {Pic}(X) = \mathbb {Z}H$$ Pic ( X ) = Z H , and let $$C\in |H|$$ C ∈ | H | be a smooth curve of genus g. We give an upper bound on the dimension of global sections of a semistable vector bundle on C. This allows us to compute the higher rank Clifford indices of C with high genus. In particular, when $$g\ge r^2\ge 4$$ g ≥ r 2 ≥ 4 , the rank r Clifford index of C can be computed by the restriction of Lazarsfeld–Mukai bundles on X corresponding to line bundles on the curve C. This is a generalization of the result by Green and Lazarsfeld for curves on K3 surfaces to higher rank vector bundles. We also apply the same method to the projective plane and show that the rank r Clifford index of a degree $$d(\ge 5)$$ d ( ≥ 5 ) smooth plane curve is $$d-4$$ d - 4 , which is the same as the Clifford index of the curve.

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Vertical clinging and leaping induced evolutionary rate shifts in postcranial evolution of tamarins and marmosets (Primates, Callitrichidae)

BMC Ecology and Evolution ◽

10.1186/s12862-021-01848-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Léo Botton-Divet ◽

John A. Nyakatura

Keyword(s):

Elbow Joint ◽

Evolutionary Rate ◽

Large Diameter ◽

Morphological Diversity ◽

Locomotor Behavior ◽

Shape Descriptors ◽

High Affinity ◽

Associated Species ◽

Future Work ◽

Shape And Size

Abstract Background Callitrichids comprise a diverse group of platyrrhine monkeys that are present across South and Central America. Their secondarily evolved small size and pointed claws allow them to cling to vertical trunks of a large diameter. Within callitrichids, lineages with a high affinity for vertical supports often engage in trunk-to-trunk leaping. This vertical clinging and leaping (VCL) differs from horizontal leaping (HL) in terms of the functional demands imposed on the musculoskeletal system, all the more so as HL often occurs on small compliant terminal branches. We used quantified shape descriptors (3D geometric morphometrics) and phylogenetically-informed analyses to investigate the evolution of the shape and size of the humerus and femur, and how this variation reflects locomotor behavior within Callitrichidae. Results The humerus of VCL-associated species has a narrower trochlea compared with HL species. It is hypothesized that this contributes to greater elbow mobility. The wider trochlea in HL species appears to correspondingly provide greater stability to the elbow joint. The femur in VCL species has a smaller head and laterally-oriented distal condyles, possibly to reduce stresses during clinging. Similarly, the expanded lesser trochanters visible in VCL species provide a greater lever for the leg retractors and are thus also interpreted as an adaptation to clinging. Evolutionary rate shifts to faster shape and size changes of humerus and femur occurred in the Leontocebus clade when a shift to slower rates occurred in the Saguinus clade. Conclusions Based on the study of evolutionary rate shifts, the transition to VCL behavior within callitrichids (specifically the Leontocebus clade) appears to have been an opportunity for radiation, rather than a specialization that imposed constraints on morphological diversity. The study of the evolution of callitrichids suffers from a lack of comparative analyses of limb mechanics during trunk-to-trunk leaping, and future work in this direction would be of great interest.

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Molecular epidemiology of coxsackievirus A16 circulating in children in Beijing, China from 2010 to 2019

World Journal of Pediatrics ◽

10.1007/s12519-021-00451-y ◽

2021 ◽

Author(s):

Ya-Fang Hu ◽

Li-Ping Jia ◽

Fang-Yuan Yu ◽

Li-Ying Liu ◽

Qin-Wei Song ◽

...

Keyword(s):

Molecular Epidemiology ◽

Evolutionary Rate ◽

Foot And Mouth Disease ◽

Recent Common Ancestor ◽

Rt Pcr ◽

Coxsackievirus A16 ◽

Most Recent Common Ancestor ◽

Etiological Agents ◽

High Level ◽

And Control

Abstract Background Coxsackievirus A16 (CVA16) is one of the major etiological agents of hand, foot and mouth disease (HFMD). This study aimed to investigate the molecular epidemiology and evolutionary characteristics of CVA16. Methods Throat swabs were collected from children with HFMD and suspected HFMD during 2010–2019. Enteroviruses (EVs) were detected and typed by real-time reverse transcription-polymerase chain reaction (RT-PCR) and RT-PCR. The genotype, evolutionary rate, the most recent common ancestor, population dynamics and selection pressure of CVA16 were analyzed based on viral protein gene (VP1) by bioinformatics software. Results A total of 4709 throat swabs were screened. EVs were detected in 3180 samples and 814 were CVA16 positive. More than 81% of CVA16-positive children were under 5 years old. The prevalence of CVA16 showed obvious periodic fluctuations with a high level during 2010–2012 followed by an apparent decline during 2013–2017. However, the activities of CVA16 increased gradually during 2018–2019. All the Beijing CVA16 strains belonged to sub-genotype B1, and B1b was the dominant strain. One B1c strain was detected in Beijing for the first time in 2016. The estimated mean evolutionary rate of VP1 gene was 4.49 × 10–3 substitution/site/year. Methionine gradually fixed at site-23 of VP1 since 2012. Two sites were detected under episodic positive selection, one of which (site-223) located in neutralizing linear epitope PEP71. Conclusions The dominant strains of CVA16 belonged to clade B1b and evolved in a fast evolutionary rate during 2010–2019 in Beijing. To provide more favorable data for HFMD prevention and control, it is necessary to keep attention on molecular epidemiological and evolutionary characteristics of CVA16.

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Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far?

Viruses ◽

10.3390/v13071192 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1192

Author(s):

Ivana Lazarevic ◽

Vera Pravica ◽

Danijela Miljanovic ◽

Maja Cupic

Keyword(s):

Immune Evasion ◽

Human Population ◽

Evolutionary Rate ◽

Spike Protein ◽

Close Monitoring ◽

Global Level ◽

Therapeutic Application ◽

Neutralization Capacity ◽

Rapid Transmission ◽

Potential Impact

Despite the slow evolutionary rate of SARS-CoV-2 relative to other RNA viruses, its massive and rapid transmission during the COVID-19 pandemic has enabled it to acquire significant genetic diversity since it first entered the human population. This led to the emergence of numerous variants, some of them recently being labeled “variants of concern” (VOC), due to their potential impact on transmission, morbidity/mortality, and the evasion of neutralization by antibodies elicited by infection, vaccination, or therapeutic application. The potential to evade neutralization is the result of diversity of the target epitopes generated by the accumulation of mutations in the spike protein. While three globally recognized VOCs (Alpha or B.1.1.7, Beta or B.1.351, and Gamma or P.1) remain sensitive to neutralization albeit at reduced levels by the sera of convalescent individuals and recipients of several anti-COVID19 vaccines, the effect of spike variability is much more evident on the neutralization capacity of monoclonal antibodies. The newly recognized VOC Delta or lineage B.1.617.2, as well as locally accepted VOCs (Epsilon or B.1.427/29-US and B1.1.7 with the E484K-UK) are indicating the necessity of close monitoring of new variants on a global level. The VOCs characteristics, their mutational patterns, and the role mutations play in immune evasion are summarized in this review.

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