Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications

One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist; some, if not all, of these features would be relics of the primary genetic information. Based on this assumption, we analyzed the pattern of frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides of the whole-genome sequences from 458 species (including archaea, bacteria, and eukaryotes). Also, we studied the phenomenon of strand symmetry in these genomes. The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon that may contribute to frequency conservation. We propose a new hypothesis for the origin of strand symmetry and frequency conservation as well as for the constitution of early genomes. We conclude that the phenomena of strand symmetry and the pattern of frequency conservation would be original features of the primary genetic information

Time and Location Aware Mobile Data Pricing

Mobile users' correlated mobility and data consumption patterns often lead to severe cellular network congestion in peak hours and hot spots. This paper presents an optimal design of time and location aware mobile data pricing, which incentivizes users to smooth traffic and reduce network congestion. We derive the optimal pricing scheme through analyzing a two-stage decision process, where the operator determines the time and location aware prices by minimizing his total cost in Stage I, and each mobile user schedules his mobile traffic by maximizing his payoff (i.e., utility minus payment) in Stage II. We formulate the two-stage decision problem as a bilevel optimization problem, and propose a derivative-free algorithm to solve the problem for any increasing concave user utility functions. We further develop low complexity algorithms for the commonly used logarithmic and linear utility functions. The optimal pricing scheme ensures a win-win situation for the operator and users. Simulations show that the operator can reduce the cost by up to 97.52% in the logarithmic utility case and 98.70% in the linear utility case, and users can increase their payoff by up to 79.69% and 106.10% for the two types of utilities, respectively, comparing with a time and location independent pricing benchmark. Our study suggests that the operator should provide price discounts at less crowded time slots and locations, and the discounts need to be significant when the operator's cost of provisioning excessive traffic is high or users' willingness to delay traffic is low.Comment: This manuscript serves as the online technical report of the article accepted by IEEE Transactions on Mobile Computin

A Kinetic Model for Cell Damage Caused by Oligomer Formation

It is well-known that the formation of amyloid fiber may cause invertible damage to cells, while the underlying mechanism has not been fully uncovered. In this paper, we construct a mathematical model, consisting of infinite ODEs in the form of mass-action equations together with two reaction-convection PDEs, and then simplify it to a system of 5 ODEs by using the maximum entropy principle. This model is based on four simple assumptions, one of which is that cell damage is raised by oligomers rather than mature fibrils. With the simplified model, the effects of nucleation and elongation, fragmentation, protein and seeds concentrations on amyloid formation and cell damage are extensively explored and compared with experiments. We hope that our results can provide a valuable insight into the processes of amyloid formation and cell damage thus raised.Comment: 16 pages+ 5 figures for maintext; 8 pages+ 4 figures for Supporting Material