Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.     

COUPLING EFFECTS OF VOID SHAPE AND VOID SIZE ON THE GROWTH OF AN ELLIPTIC VOID IN A FIBER-REINFORCED HYPER-ELASTIC THIN PLATE

The growth of a prolate or oblate elliptic micro-void in a fiber reinforced anisotropic incompressible hyper-elastic rectangular thin plate subjected to uniaxial extensions is studied within the framework of finite elasticity. Coupling effects of void shape and void size on the growth of the void are paid special attention to. The deformation function of the plate with an isolated elliptic void is given, which is expressed by two parameters to solve the differential equation. The solution is approximately obtained from the minimum potential energy principle. Deformation curves for the void with a wide range of void aspect ratios and the stress distributions on the surface of the void have been obtained by numerical computation. The growth behavior of the void and the characteristics of stress distributions on the surface of the void are captured. The combined effects of void size and void shape on the growth of the void in the thin plate are discussed. The maximum stresses for the void with different sizes and different void aspect ratios are compared.     

Random frog: An efficient reversible jump Markov Chain Monte Carlo-like approach for variable selection with applications to gene selection and disease classification

The identification of disease-relevant genes represents a challenge in microarray-based disease diagnosis where the sample size is often limited. Among established methods, reversible jump Markov Chain Monte Carlo (RJMCMC) methods have proven to be quite promising for variable selection. However, the design and application of an RJMCMC algorithm requires, for example, special criteria for prior distributions. Also, the simulation from joint posterior distributions of models is computationally extensive, and may even be mathematically intractable. These disadvantages may limit the applications of RJMCMC algorithms. Therefore, the development of algorithms that possess the advantages of RJMCMC methods and are also efficient and easy to follow for selecting disease-associated genes is required. Here we report a RJMCMC-like method, called random frog that possesses the advantages of RJMCMC methods and is much easier to implement. Using the colon and the estrogen gene expression datasets, we show that random frog is effective in identifying discriminating genes. The top 2 ranked genes for colon and estrogen are Z50753, U00968, and Y10871_at, Z22536_at, respectively. (The source codes with GNU General Public License Version 2.0 are freely available to non-commercial users at: http://code.google.com/p/randomfrog/.)     

Charge generation and electrostatic equilibrium for single granules during sliding

Electrostatic phenomena are commonly observed in the processing of solids. However, the working mechanism of electrostatic charge generation for single granules and particularly, their electrostatic equilibria have not been properly understood. In this work, repeated-sliding charging experiments with single granules were investigated for their electrostatic generation particularly from the perspective of triboelectrification equilibrium. Factors including granule length-ratio, sliding face shape, sliding times, sliding area, sliding velocity, front-facing edge, and sliding-plate inclined-angle were found to have an obvious effect on granule charge generation. Length-ratio and sliding area have significant effects as the granules evolved toward an equilibrium state. Equilibrium charge is suggested as a variable expressing the charging propensity of the material. In addition, under the same working conditions, a semi-cylindrical granule generates greater charge than a rectangular granule.     

Physically cross‐linked networks of POSS‐capped poly(acrylate amide)s: Synthesis,morphologies, and shape memory behavior

In this work, we synthesized a novel organic–inorganic semitelechelic polymer from polyhedral oligomeric silsesquioxane (POSS) and poly(acrylate amide) (PAA) via reversible addition‐fragmentation chain transfer (RAFT) polymerization. The organic–inorganic semitelechelic polymers have been characterized by means of nuclear magnetic resonance spectroscopy, thermal gravimetric analysis, and dynamic mechanical thermal analysis. It was found that capping POSS groups to the single ends of PAA chains caused a series of significant changes in the morphologies and thermomechanical properties of the polymer. The organic–inorganic semitelechelics were microphase‐separated; the POSS microdomains were formed via the POSS–POSS interactions. In a selective solvent (e.g., methanol), the organic–inorganic semitelechelics can be self‐assembled into the micelle‐like nanoobjects. Compared to plain PAA, the POSS‐capped PAAs significantly displayed improved surface hydrophobicity as evidenced by the measurements of static contact angles and surface atomic force microscopy. More importantly, the organic–inorganic semitelechelics displayed typical shape memory properties, which was in marked contrast to plain PAA. The shape memory behavior is attributable to the formation of the physically cross‐linked networks from the combination of the POSS–POSS interactions with the intermolecular hydrogen‐bonding interactions in the organic–inorganic semitelechelics. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 587–600     

Shape memory induced structural evolution of high performance copolyimides

In this work, two kinds of high temperature shape memory copolyimides were prepared and the shape memory cycles induced structural evolution of macromolecular chains was investigated in detail. The glass transition temperature (T_g) of poly(benzoxazole‐co‐imide) (PI1) and poly(benzimidazole‐co‐imide) (PI2) are 280 °C and 355 °C, respectively. The results show that PI1 could keep stable macromolecular chain structure under shape memory cycles and exhibit outstanding shape memory performance (R_f > 98%, R_r > 97%) under different stretch condition. Whereas, shape memory cycles induced orientation with more ordered macromolecular chains packing is formed for PI2 after several thermal mechanical cycles, which strongly affect physical crosslinking points, thermal mechanical properties as well as shape memory behaviors. The study on macroscopic property and microscopic structure evolution will promote a better understanding of the shape memory effect of polyimides and accelerate development of high performance polyimides for shape memory applications. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 3858–3867     

A maximum-efficiency-first multi-path route selection strategy for optical burst switching networks

In this paper, the impact of a path selection on other existing paths in optical burst switching (OBS) networks is studied by analyzing the contention among different traffic streams and the interaction between the route selection and traffic load balance. The results show that there exists a mutual reinforcement interaction among the traffic load of a path, the path burst loss ratio and the contention ability of the path when burst loss ratio based multi-path selection strategies are adopted, which may increase the unbalance of traffic and lead to severe congestion further. A maximum-efficiency-first multi-path selection strategy, which considers the performance of the burst flows and the impact of a path selection on existing OBS paths at the same time by a combined metric of route efficiency, is proposed to maximize the utility of the burst flows and minimize the increment of lost throughput on the path. The performance of the proposed multi-path selection strategy is evaluated through simulation. The results show that the presented strategy obviously outperforms the least burst loss ratio strategy and shortest path first strategy in terms of the burst loss ratio in the practical unbalanced background traffic, especially when the network is heavily loaded.     

Synthesis and design of polyurethane and its nanocomposites derived from canola-castor oil: Mechanical,thermal and shape memory properties

The recent global pandemic and its tremendous effect on the price fluctuations of crude oil illustrates the side effects of petroleum dependency more evident than ever. Over the past decades, both academic and industrial communities spared endless efforts in order to replace petroleum-based materials with bio-derived resources. In the current study, a series of shape memory polymer composites (SMPC's) was synthesized from epoxidized vegetable oils, namely canola oil and castor oil fatty acids (COFA's) as a 100% bio-based polyol and isophorone diisocyanate (IPDI) as an isocyanate using a solvent/catalyst-free method in order to eventuate polyurethanes (PU's). Thereafter, graphene oxide (GO) nanoplatelets were synthesized and embedded in the neat PU in order to overcome the thermomechanical drawbacks of the neat matrix. The chemical structure of the synthesized components, as well as the dispersion and distribution levels of the nanoparticles, was characterized. In the following, thermal and mechanical properties as well as shape memory behavior of the specimens were comprehensively investigated. Likewise, the thermal conductivity was determined. This study proves that synthesized PU's based on vegetable oil polyols, including graphene nanoparticles, exhibit proper thermal and mechanical properties, which make them stand as a potential candidate to compete with traditional petroleum-based SMPC's.