Modeling Gene Networks in Saccharomyces cerevisiae

Detailed and innovative analysis of gene regulatory network structures may reveal novel insights to biological mechanisms. Here we study how gene regulatory network in Saccharomyces cerevisiae can differ under aerobic and anaerobic conditions. To achieve this, we discretized the gene expression profiles and calculated the self-entropy of down- and upregulation of gene expression as well as joint entropy. Based on these quantities the uncertainty coefficient was calculated for each gene triplet, following which, separate gene logic networks were constructed for the aerobic and anaerobic conditions. Four structural parameters such as average degree, average clustering coefficient, average shortest path, and average betweenness were used to compare the structure of the corresponding aerobic and anaerobic logic networks. Five genes were identified to be putative key components of the two energy metabolisms. Furthermore, community analysis using the Newman fast algorithm revealed two significant communities for the aerobic but only one for the anaerobic network. David Gene Functional Classification suggests that, under aerobic conditions, one such community reflects the cell cycle and cell replication, while the other one is linked to the mitochondrial respiratory chain function

FashionLOGO: Prompting Multimodal Large Language Models for Fashion Logo Embeddings

Logo embedding plays a crucial role in various e-commerce applications by facilitating image retrieval or recognition, such as intellectual property protection and product search. However, current methods treat logo embedding as a purely visual problem, which may limit their performance in real-world scenarios. A notable issue is that the textual knowledge embedded in logo images has not been adequately explored. Therefore, we propose a novel approach that leverages textual knowledge as an auxiliary to improve the robustness of logo embedding. The emerging Multimodal Large Language Models (MLLMs) have demonstrated remarkable capabilities in both visual and textual understanding and could become valuable visual assistants in understanding logo images. Inspired by this observation, our proposed method, FashionLOGO, aims to utilize MLLMs to enhance fashion logo embedding. We explore how MLLMs can improve logo embedding by prompting them to generate explicit textual knowledge through three types of prompts, including image OCR, brief captions, and detailed descriptions prompts, in a zero-shot setting. We adopt a cross-attention transformer to enable image embedding queries to learn supplementary knowledge from textual embeddings automatically. To reduce computational costs, we only use the image embedding model in the inference stage, similar to traditional inference pipelines. Our extensive experiments on three real-world datasets demonstrate that FashionLOGO learns generalized and robust logo embeddings, achieving state-of-the-art performance in all benchmark datasets. Furthermore, we conduct comprehensive ablation studies to demonstrate the performance improvements resulting from the introduction of MLLMs

Identifying veraison process of colored wine grapes in field conditions combining deep learning and image analysis

Acknowledgments This work was supported by the National Key R&D Program Project of China (Grant No. 2019YFD1002500) and Guangxi Key R&D Program Project (Grant No. Gui Ke AB21076001) The authors would like to thank the anonymous reviewers for their helpful comments and suggestions.Peer reviewedPostprin

Development of a mobile application for identification of grapevine (Vitis vinifera L.) cultivars via deep learning

Acknowledgements: The authors would like to express their gratitude to the Teaching Experiment Farm of Ningxia University, for their kind help. This study was supported by the Key R & D projects of Ningxia Hui Autonomous Region (Grant No. 2019BBF02013)Peer reviewedPublisher PD

Segmentation of field grape bunches via an improved pyramid scene parsing network

With the continuous expansion of wine grape planting areas, the mechanization and intelligence of grape harvesting have gradually become the future development trend. In order to guide the picking robot to pick grapes more efficiently in the vineyard, this study proposed a grape bunches segmentation method based on Pyramid Scene Parsing Network (PSPNet) deep semantic segmentation network for different varieties of grapes in the natural field environments. To this end, the Convolutional Block Attention Module (CBAM) attention mechanism and the atrous convolution were first embedded in the backbone feature extraction network of the PSPNet model to improve the feature extraction capability. Meanwhile, the proposed model also improved the PSPNet semantic segmentation model by fusing multiple feature layers (with more contextual information) extracted by the backbone network. The improved PSPNet was compared against the original PSPNet on a newly collected grape image dataset, and it was shown that the improved PSPNet model had an Intersection-over-Union (IoU) and Pixel Accuracy (PA) of 87.42% and 95.73%, respectively, implying an improvement of 4.36% and 9.95% over the original PSPNet model. The improved PSPNet was also compared against the state-of-the-art DeepLab-V3+ and U-Net in terms of IoU, PA, computation efficiency and robustness, and showed promising performance. It is concluded that the improved PSPNet can quickly and accurately segment grape bunches of different varieties in the natural field environments, which provides a certain technical basis for intelligent harvesting by grape picking robots

Sentinel-2 satellite imagery for urban land cover classification by optimized random forest classifier

Land cover classification is able to reflect the potential natural and social process in urban development, providing vital information to stakeholders. Recent solutions on land cover classification are generally addressed by remotely sensed imagery and supervised classification methods. However, a high-performance classifier is desirable but challenging due to the existence of model hyperparameters. Conventional approaches generally rely on manual tuning, which is time-consuming and far from satisfying. Therefore, this work aims to propose a systematic method to automatically tune the hyperparameters by Bayesian parameter optimization for the random forest classifier. The recently launched Sentinel-2A/B satellites are drawn to provide the remote sensing imageries for land cover classification case study in Beijing, China, which have the best spectral/spatial resolutions among the freely available satellites. The improved random forest with Bayesian parameter optimization is compared against the support vector machine (SVM) and random forest (RF) with default hyperparameters by discriminating five land cover classes including building, tree, road, water and crop field. Comparative experimental results show that the optimized RF classifier outperforms the conventional SVM and the RF with default hyperparameters in terms of accuracy, precision and recall. The effects of band/feature number and the band usefulness are also assessed. It is envisaged that the improved classifier for Sentinel-2 satellite image processing can find a wide range of applications where high-resolution satellite imagery classification is applicable

Chitosan/Silver Nanoparticle/Graphene Oxide Nanocomposites with Multi-Drug Release, Antimicrobial, and Photothermal Conversion Functions

In this work, we designed and fabricated a multifunctional nanocomposite system that consists of chitosan, raspberry-like silver nanoparticles, and graphene oxide. The room temperature atmospheric pressure microplasma (RT-APM) process provides a rapid, facile, and environmentally-friendly method for introducing silver nanoparticles into the composite system. Our composite can achieve a pH controlled single and/or dual drug release. Under pH 7.4 for methyl blue loaded on chitosan, the drug release profile features a burst release during the first 10 h, followed by a more stabilized release of 70–80% after 40–50 h. For fluorescein sodium loaded on graphene oxide, the drug release only reached 45% towards the end of 240 h. When the composite acted as a dual drug release system, the interaction of fluorescein sodium and methyl blue slowed down the methyl blue release rate. Under pH 4, both single and dual drug systems showed a much higher release rate. In addition, our composite system demonstrated strong antibacterial abilities against E. coli and S. aureus, as well as an excellent photothermal conversion effect under irradiation of near infrared lasers. The photothermal conversion efficiency can be controlled by the laser power. These unique functionalities of our nanocomposite point to its potential application in multiple areas, such as multimodal therapeutics in healthcare, water treatment, and anti-microbials, among others

Electronic Structure, Surface Doping, and Optical Response in Epitaxial WSe2 Thin Films

High quality WSe2 films have been grown on bilayer graphene (BLG) with layer-by-layer control of thickness using molecular beam epitaxy (MBE). The combination of angle-resolved photoemission (ARPES), scanning tunneling microscopy/spectroscopy (STM/STS), and optical absorption measurements reveal the atomic and electronic structures evolution and optical response of WSe2/BLG. We observe that a bilayer of WSe2 is a direct bandgap semiconductor, when integrated in a BLG-based heterostructure, thus shifting the direct-indirect band gap crossover to trilayer WSe2. In the monolayer limit, WSe2 shows a spin-splitting of 475 meV in the valence band at the K point, the largest value observed among all the MX2 (M = Mo, W; X = S, Se) materials. The exciton binding energy of monolayer-WSe2/BLG is found to be 0.21 eV, a value that is orders of magnitude larger than that of conventional 3D semiconductors, yet small as compared to other 2D transition metal dichalcogennides (TMDCs) semiconductors. Finally, our finding regarding the overall modification of the electronic structure by an alkali metal surface electron doping opens a route to further control the electronic properties of TMDCs