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Background and Aims Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models. Methods We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing. Key Results Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models. Conclusions Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept. [ABSTRACT FROM AUTHOR]

Patterned materials on substrates are of great importance for a wide variety of applications. In solution-based approaches to material patterning, fluidic flow is inevitable. Here we demonstrate not only the importance of fluidic behavior but also the methodology of engineering the flow pattern to guide the material crystallization and assembly. We show by both experiment and simulation that substrate heating, which is generally used to accelerate evaporation, produces irregular complex vortexes. Instead, a top-heating–bottom-cooling (THBC) set-up offers an inverse temperature gradient and results in a single Marangoni vortex, which is desired for ordered nanomaterial patterning near the contact line. We then realize the fabrication of large-scale patterns of iodide perovskite crystals on different substrates under THBC conditions. We further demonstrate that harnessing the flow behavior is a general strategy with great feasibility to pattern various functional materials ranging from inorganic, organic, hybrid to biological categories on different substrates, presenting great potential for practical applications. [ABSTRACT FROM AUTHOR]

The total generalized variation (TGV) denoising model is the extension of the total variation (TV) model and is capable of avoiding the staircase artifacts of the TV model. However, the TGV model independently disposes the pixels, ignoring the structural similarity prior of the processed image. Thus, the TGV model is not robust to high-amplitude noise. The motivation of this paper is to employ the structural similarity and improve the TGV denoising effect. By introducing the overlapping group sparsity to the TGV model, a new improved TGV model is then proposed, exploring both the first-order and second-order neighborhood differential gradient information to improve the robustness of the TGV to heavy noise pollution. To solve the proposed model, we adopted the accelerated alternating direction method of multipliers (ADMM), in which the multi-constrained problem is divided into several sub-problems. To avoid large-scale matrix computations in the spatial domain, we regard the differential operators as the convolution form, and thus the fast Fourier transform and the convolution theorem are employed to solve the proposed model efficiently. Finally, experiments were conducted on several seismic signals under different types of noise to verify the proposed method. The findings are listed as follows (1). The proposed model is particularly good at removing the heavy noise in smooth areas (2). The accelerated ADMM with a restart process is capable of solving the proposed model and is much faster than the traditional ADMM (3). The group size should be chosen properly to arrive the best performance of the proposed method. [ABSTRACT FROM AUTHOR]