Defective Media Research Articles

Hierarchical Microbial Functions Prediction by Graph Aggregated Embedding.

Matching 16S rRNA gene sequencing data to a metabolic reference database is a meaningful way to predict the metabolic function of bacteria and archaea, bringing greater insight to the working of the microbial community. However, some operational taxonomy units (OTUs) cannot be functionally profiled, especially for microbial communities from non-human samples cultured in defective media. Therefore, we herein report the development of Hierarchical micrObial functions Prediction by graph aggregated Embedding (HOPE), which utilizes co-occurring patterns and nucleotide sequences to predict microbial functions. HOPE integrates topological structures of microbial co-occurrence networks with k-mer compositions of OTU sequences and embeds them into a lower-dimensional continuous latent space, while maximally preserving topological relationships among OTUs. The high imbalance among KEGG Orthology (KO) functions of microbes is recognized in our framework that usually yields poor performance. A hierarchical multitask learning module is used in HOPE to alleviate the challenge brought by the long-tailed distribution among classes. To test the performance of HOPE, we compare it with HOPE-one, HOPE-seq, and GraphSAGE, respectively, in three microbial metagenomic 16s rRNA sequencing datasets, including abalone gut, human gut, and gut of Penaeus monodon. Experiments demonstrate that HOPE outperforms baselines on almost all indexes in all experiments. Furthermore, HOPE reveals significant generalization ability. HOPE's basic idea is suitable for other related scenarios, such as the prediction of gene function based on gene co-expression networks. The source code of HOPE is freely available at https://github.com/adrift00/HOPE.

An Intense Wave in Defective Media Containing Both Quadratic and Modular Nonlinearities: Shock Waves, Harmonics, and Nondestructive Testing

The observed nonclassical power-law dependence of the amplitude of the second harmonic wave on the amplitude of a harmonic pump wave is explained as a phenomenon associated with two types of nonlinearity in a structurally inhomogeneous medium. An approach to solving the inverse problem of determining the nonlinearity parameters and the exponent in the above-mentioned dependence is demonstrated. To describe the effects of strongly pronounced nonlinearity, equations containing a double nonlinearity and generalizing the Hopf and Burgers equations are proposed. The possibility of their exact linearization is demonstrated. The profiles, spectral composition, and average wave intensity in such doubly nonlinear media are calculated. The shape of the shock front is found, and its width is estimated. The wave energy losses that depend on both nonlinearity parameters—quadratic and modular—are calculated.

Simulation of the mechanical properties of nanostructured porous ceramics

A nonclassical model is developed to describe the deformation of nanostructured ceramics. The model takes into account the scale effects and can be used to determine the effective elastic moduli of such ceramics with allowance for the grain size, the damage level (porosity), and the adhesion parameters characterizing the intergrain contact quality. This model is based on a particular version of the gradient theory of defective media, in which the free strain tensor is determined by the free volume change strains and the continuum model of adhesion interactions is consistent with a chosen kinematic model. The effective characteristics of ceramics are determined with the gradient cohesion-adhesion model using the modified three-phase Eshelby method. Examples of simulating the effective elastic moduli are given, and they demonstrate the efficiency of the model and its adequacy to the well-known experimental data.