Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines

Carbohydrate-binding proteins are proteins that can interact with sugar chains but do not modify them. They are involved in many physiological functions, and we have developed a method for predicting them from their amino acid sequences. Our method is based on support vector machines (SVMs). We first clarified the definition of carbohydrate-binding proteins and then constructed positive and negative datasets with which the SVMs were trained. By applying the leave-one-out test to these datasets, our method delivered 0.92 of the area under the receiver operating characteristic (ROC) curve. We also examined two amino acid grouping methods that enable effective learning of sequence patterns and evaluated the performance of these methods. When we applied our method in combination with the homology-based prediction method to the annotated human genome database, H-invDB, we found that the true positive rate of prediction was improved

Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus

The AP2/ERF superfamily, one of the most important transcription factor families, plays crucial roles in response to biotic and abiotic stresses. So far, a comprehensive evolutionary inference of its origination and expansion has not been available. Here, we identified 515 AP2/ERF genes in B. napus, a neo-tetraploid forming ~7500 years ago, and found that 82.14% of them were duplicated in the tetraploidization. A prominent subgenome bias was revealed in gene expression, tissue-specific, and gene conversion. Moreover, a large-scale analysis across plants and alga suggested that this superfamily could have been originated from AP2 family, expanding to form other families (ERF, and RAV). This process was accompanied by duplicating and/or alternative deleting AP2 domain, intragenic domain sequence conversion, and/or by acquiring other domains, resulting in copy number variations, alternatively contributing to functional innovation. We found that significant positive selection occurred at certain critical nodes during the evolution of land plants, possibly responding to changing environment. In conclusion, the present research revealed origination, functional innovation, and evolutionary trajectory of the AP2/ERF superfamily, contributing to understanding their roles in plant stress tolerance

Train Operational Plan Optimization for Urban Rail Transit Lines Considering Circulation Balance

The passenger demand of urban rail transit (URT) lines often present asymmetric tidal time-varying characteristics. To match the demand fluctuation, the train operational plan (TOP) generally has asymmetric bi-directional frequency/headway setting and imbalanced circulation, leading to high operation cost. This paper incorporates circulation balance into TOP optimization to balance the bi-directional arrival, departure, circulation, and resource utilization, and reduce the overall operation cost. Based on time-varying section demand and predetermined service level, bi-directional stepped maximum headway functions are collaboratively constructed, and then the circulation process is described by the trip flow circulation network that is formulated as a cost-oriented integer linear programming model. Using the optimized frequency setting, the final TOP is obtained by a two-stage approach to successively solve the schedule and rolling stock circulations at terminals. The case study based on an URT line in Shenzhen indicates that the proposed approach can not only ensure the required service level for travel demand, but also improve the efficiency of circulation and utilization, and effectively reduce the overall operation cost. The proposed approach provides an effective technique to keep balanced, stable and sustainable operation for URT lines

Real-Time Monitoring and Step-by-Step Guidance for Transapical Mitral Valve Edge-to-Edge Repair Using Transesophageal Echocardiography

MitraClip edge-to-edge (E2E) repair system is the only transcatheter device recommended in the current guidelines for treating mitral regurgitation (MR). The percutaneous femoral venous transseptal access of MitraClip requires a complex steerable delivery system and may thus be technically complex to optimally position and deploy the clip onto the mitral valve. A transapical approach for E2E repair has been devised to treat MR for the ease of operation (ValveClamp system, Hanyu Medical Technology, Shanghai). The first-in-human study of ValveClamp has demonstrated its early feasibility and effectiveness for the treatment of patients with degenerative MR. Transesophageal echocardiography (TEE) is the only imaging modality required for intraoperative guidance of ValveClamp implantation. Successful implantation depends on accurate localization and orientation of the clamp and efficient intraoperative communication between the echocardiographer and the intervention team. Thus, the focus of this review is on elaborating how two-dimensional (2D) and three-dimensional (3D) TEE are used in clinical practice to guide ValveClamp implantation and it may facilitate the understanding of simplicity and safety of this novel procedure. We also describe the implementation of several novel advancements in 3D TEE imaging, which improve the confidence of image interpretation for intraoperative guidance and expedite implantation times

RNA-Seq Profiling Shows Divergent Gene Expression Patterns in Arabidopsis Grown under Different Densities

Plants growing under high-density (HD) conditions experience increased competition for water, nutrients, and light, possibly leading to changes in size, biomass, morphology, and productivity. However, no research has focused on the relationship between whole-genome expression patterns and growth density. Here, we performed whole-genome RNA sequencing to examine the gene expression patterns in Arabidopsis grown under low and high densities. Of the 20,660 detected genes, the expression levels of 98 were enhanced and 107 were repressed under HD growth. Further analysis revealed that changes in density influenced metabolism- and stimulus-related genes the most. Furthermore, HD growth led to a shade avoidance phenotype, represented by upward growth and a reduction in rosette leaves. Moreover, a cluster of glutaredoxin genes, GRXS3, 4, 5, 7, and 8, were significantly down-regulated under high density, suggesting that high density affects plant growth mainly by nitrate limitation

Segmentation of Echocardiography Based on Deep Learning Model

In order to achieve the classification of mitral regurgitation, a deep learning network VDS-UNET was designed to automatically segment the critical regions of echocardiography with three sections of apical two-chamber, apical three-chamber, and apical four-chamber. First, an expert-labeled dataset of 153 echocardiographic videos and 2183 images from 49 subjects was constructed. Then, the convolution layer in the VGG16 network was used to replace the contraction path in the original UNet network to extract image features, and depth supervision was added to the expansion path to achieve the segmentation of LA, LV, and MV. The results showed that the Dice coefficients of LA, LV, and MV were 0.935, 0.915, and 0.757, respectively. The proposed deep learning network can achieve simultaneous and accurate segmentation of LA, LV, and MV in multi-section echocardiography, laying a foundation for quantitative measurement of clinical parameters related to mitral regurgitation

Influence of Industrialization and Environmental Protection on Environmental Pollution: A Case Study of Taihu Lake, China

In order to quantitatively study the effect of environmental protection in China since the twenty-first century and the environmental pollution projected for the next ten years (under the model of extensive economic development), this paper establishes a Bayesian regulation back propagation neural network (BRBPNN) to analyze the typical pollutants (i.e., cadmium (Cd) and benzopyrene (BaP)) for Taihu Lake, a typical Chinese freshwater lake. For the periods 1950⁻2003 and 1950⁻2015, the neural network model estimated the BaP concentration for the database with Nash-Sutcliffe model efficiency (NS) = 0.99 and 0.99 and root-mean-square error (RMSE) = 3.1 and 9.3 for the total database and the Cd concentration for the database with NS = 0.93 and 0.98 and RMSE = 45.4 and 65.7 for the total database, respectively. In the model of extensive economic development, the concentration of pollutants in the sediments of Taihu reached the maximum value at the end of the twentieth century and early twenty-first century, and there was an inflection point. After the early twenty-first century, the concentration of pollutants was controlled under various environmental policies and measures. In 2015, the environmental protection ratio of Cd and BaP reached 52% and 89%, respectively. Without environmental protection measures, the concentrations of Cd and BaP obtained from the neural network model is projected to reach 2015.5 μg kg−1 and 407.8 ng g−1, respectively, in 2030. Based on the results of this study, the Chinese government will need to invest more money and energy to clean up the environment

Alignment of Common Wheat and Other Grass Genomes Establishes a Comparative Genomics Research Platform

Grass genomes are complicated structures as they share a common tetraploidization, and particular genomes have been further affected by extra polyploidizations. These events and the following genomic re-patternings have resulted in a complex, interweaving gene homology both within a genome, and between genomes. Accurately deciphering the structure of these complicated plant genomes would help us better understand their compositional and functional evolution at multiple scales. Here, we build on our previous research by performing a hierarchical alignment of the common wheat genome vis-à-vis eight other sequenced grass genomes with most up-to-date assemblies, and annotations. With this data, we constructed a list of the homologous genes, and then, in a layer-by-layer process, separated their orthology, and paralogy that were established by speciations and recursive polyploidizations, respectively. Compared with the other grasses, the far fewer collinear outparalogous genes within each of three subgenomes of common wheat suggest that homoeologous recombination, and genomic fractionation should have occurred after its formation. In sum, this work contributes to the establishment of an important and timely comparative genomics platform for researchers in the grass community and possibly beyond. Homologous gene list can be found in Supplemental material