Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast.

To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, live-cell, and single-molecule resolution microscopy approaches in budding yeast to demonstrate that basket formation is dependent on RNA polymerase II transcription and subsequent mRNP processing. We further show that while all NPCs can bind Mlp1, baskets assemble only on a subset of nucleoplasmic NPCs, and these basket-containing NPCs associate a distinct protein and RNA interactome. Taken together, our data point toward NPC heterogeneity and an RNA-dependent mechanism for functionalization of NPCs in budding yeast through nuclear basket assembly.

HN-PPISP: a hybrid network based on MLP-Mixer for protein-protein interaction site prediction.

MOTIVATION: Biological experimental approaches to protein-protein interaction (PPI) site prediction are critical for understanding the mechanisms of biochemical processes but are time-consuming and laborious. With the development of Deep Learning (DL) techniques, the most popular Convolutional Neural Networks (CNN)-based methods have been proposed to address these problems. Although significant progress has been made, these methods still have limitations in encoding the characteristics of each amino acid in protein sequences. Current methods cannot efficiently explore the nature of Position Specific Scoring Matrix (PSSM), secondary structure and raw protein sequences by processing them all together. For PPI site prediction, how to effectively model the PPI context with attention to prediction remains an open problem. In addition, the long-distance dependencies of PPI features are important, which is very challenging for many CNN-based methods because the innate ability of CNN is difficult to outperform auto-regressive models like Transformers. RESULTS: To effectively mine the properties of PPI features, a novel hybrid neural network named HN-PPISP is proposed, which integrates a Multi-layer Perceptron Mixer (MLP-Mixer) module for local feature extraction and a two-stage multi-branch module for global feature capture. The model merits Transformer, TextCNN and Bi-LSTM as a powerful alternative for PPI site prediction. On the one hand, this is the first application of an advanced Transformer (i.e. MLP-Mixer) with a hybrid network for sequence-based PPI prediction. On the other hand, unlike existing methods that treat global features altogether, the proposed two-stage multi-branch hybrid module firstly assigns different attention scores to the input features and then encodes the feature through different branch modules. In the first stage, different improved attention modules are hybridized to extract features from the raw protein sequences, secondary structure and PSSM, respectively. In the second stage, a multi-branch network is designed to aggregate information from both branches in parallel. The two branches encode the features and extract dependencies through several operations such as TextCNN, Bi-LSTM and different activation functions. Experimental results on real-world public datasets show that our model consistently achieves state-of-the-art performance over seven remarkable baselines. AVAILABILITY: The source code of HN-PPISP model is available at https://github.com/ylxu05/HN-PPISP.

A novel gene-trap line reveals the dynamic patterns and essential roles of cysteine and glycine-rich protein 3 in zebrafish heart development and regeneration.

Mutations in cysteine and glycine-rich protein 3 (CSRP3)/muscle LIM protein (MLP), a key regulator of striated muscle function, have been linked to hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) in patients. However, the roles of CSRP3 in heart development and regeneration are not completely understood. In this study, we characterized a novel zebrafish gene-trap line, gSAIzGFFM218A, which harbors an insertion in the csrp3 genomic locus, heterozygous fish served as a csrp3 expression reporter line and homozygous fish served as a csrp3 mutant line. We discovered that csrp3 is specifically expressed in larval ventricular cardiomyocytes (CMs) and that csrp3 deficiency leads to excessive trabeculation, a common feature of CSRP3-related HCM and DCM. We further revealed that csrp3 expression increased in response to different cardiac injuries and was regulated by several signaling pathways vital for heart regeneration. Csrp3 deficiency impeded zebrafish heart regeneration by impairing CM dedifferentiation, hindering sarcomere reassembly, and reducing CM proliferation while aggravating apoptosis. Csrp3 overexpression promoted CM proliferation after injury and ameliorated the impairment of ventricle regeneration caused by pharmacological inhibition of multiple signaling pathways. Our study highlights the critical role of Csrp3 in both zebrafish heart development and regeneration, and provides a valuable animal model for further functional exploration that will shed light on the molecular pathogenesis of CSRP3-related human cardiac diseases.

Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum.

Plant defense responses to the soil-borne fungus Verticillium longisporum causing stem stripe disease on oilseed rape (Brassica napus) are poorly understood. In this study, a population of recombinant inbred lines (RILs) using the Arabidopsis accessions Sei-0 and Can-0 was established. Composite interval mapping, transcriptome data, and T-DNA mutant screening identified the NITRATE/PEPTIDE TRANSPORTER FAMILY 5.12 (AtNPF5.12) gene as being associated with disease susceptibility in Can-0. Co-immunoprecipitation revealed interaction between AtNPF5.12 and the MAJOR LATEX PROTEIN family member AtMLP6, and fluorescence microscopy confirmed this interaction in the plasma membrane and endoplasmic reticulum. CRISPR/Cas9 technology was applied to mutate the NPF5.12 and MLP6 genes in B. napus. Elevated fungal growth in the npf5.12 mlp6 double mutant of both oilseed rape and Arabidopsis demonstrated the importance of these genes in defense against V. longisporum. Colonization of this fungus depends also on available nitrates in the host root. Accordingly, the negative effect of nitrate depletion on fungal growth was less pronounced in Atnpf5.12 plants with impaired nitrate transport. In addition, suberin staining revealed involvement of the NPF5.12 and MLP6 genes in suberin barrier formation. Together, these results demonstrate a dependency on multiple plant factors that leads to successful V. longisporum root infection.

Integrating conceptual and machine learning models to enhance daily-Scale streamflow simulation and assessing climate change impact in the watersheds of the Godavari basin, India.

This study examined and addressed climate change's effects on hydrological patterns, particularly in critical places like the Godavari River basin. This study used daily gridded rainfall and temperature datasets from the Indian Meteorological Department (IMD) for model training and testing, 70% and 30%, respectively. To anticipate future hydrological shifts, the study harnessed the EC-Earth3 data, presenting an innovative methodology tailored to the unique hydrological dynamics of the Godavari River basin. The Sacramento model provided initial streamflow estimates for Kanhargaon, Nowrangpur, and Wairagarh. This approach melded traditional hydrological modeling with advanced multi-layer perceptron (MLP) capabilities. When combined with parameters like lagged rainfall, lagged streamflow, potential evapotranspiration (PET), and temperature variations, these initial outputs were further refined using the Sac-MLP model. A comparison with Sacramento revealed the superior performance of the Sac-MLP model. For instance, during training, the Nash Sutcliffe efficiency (NSE) values for the Sac-MLP witnessed an improvement from 0.610 to 0.810 in Kanhargaon, 0.580 to 0.692 in Nowrangpur, and 0.675 to 0.849 in Wairagarh. The results of the testing further corroborated these findings, as evidenced by the increase in the NSE for Kanhargaon from 0.890 to 0.910. Additionally, Nowrangpur and Wairagarh experienced notable improvements, with their NSE values rising from 0.629 to 0.785 and 0.725 to 0.902, respectively. Projections based on EC-Earth3 data across various scenarios highlighted significant shifts in rainfall and temperature patterns, especially in the far future (2071-2100). Regarding the relative change in annual streamflow, Kanhargaon projections under SSP370 and SSP585 for the far future indicate increases of 584.38% and 662.74%. Similarly, Nowrangpur and Wairagarh are projected to see increases of 98.27% and 114.98%, and 81.68% and 108.08%, respectively. This study uses EC-Earth3 estimates to demonstrate the Sac-MLP model's accuracy and importance in climate change water resource planning. The unique method for region-specific hydrological analysis provides vital insights for sustainable water resource management. This research provides a deeper understanding of climate-induced hydrological changes and a robust modeling approach for accurate predictions in changing environmental conditions.

A novel Skin lesion prediction and classification technique: ViT-GradCAM.

BACKGROUND: Skin cancer is one of the highly occurring diseases in human life. Early detection and treatment are the prime and necessary points to reduce the malignancy of infections. Deep learning techniques are supplementary tools to assist clinical experts in detecting and localizing skin lesions. Vision transformers (ViT) based on image segmentation classification using multiple classes provide fairly accurate detection and are gaining more popularity due to legitimate multiclass prediction capabilities. MATERIALS AND METHODS: In this research, we propose a new ViT Gradient-Weighted Class Activation Mapping (GradCAM) based architecture named ViT-GradCAM for detecting and classifying skin lesions by spreading ratio on the lesion's surface area. The proposed system is trained and validated using a HAM 10000 dataset by studying seven skin lesions. The database comprises 10 015 dermatoscopic images of varied sizes. The data preprocessing and data augmentation techniques are applied to overcome the class imbalance issues and improve the model's performance. RESULT: The proposed algorithm is based on ViT models that classify the dermatoscopic images into seven classes with an accuracy of 97.28%, precision of 98.51, recall of 95.2%, and an F1 score of 94.6, respectively. The proposed ViT-GradCAM obtains better and more accurate detection and classification than other state-of-the-art deep learning-based skin lesion detection models. The architecture of ViT-GradCAM is extensively visualized to highlight the actual pixels in essential regions associated with skin-specific pathologies. CONCLUSION: This research proposes an alternate solution to overcome the challenges of detecting and classifying skin lesions using ViTs and GradCAM, which play a significant role in detecting and classifying skin lesions accurately rather than relying solely on deep learning models.

Research on the Multiple Small Target Detection Methodology in Remote Sensing.

This study focuses on advancing the field of remote sensing image target detection, addressing challenges such as small target detection, complex background handling, and dense target distribution. We propose solutions based on enhancing the YOLOv7 algorithm. Firstly, we improve the multi-scale feature enhancement (MFE) method of YOLOv7, enhancing its adaptability and precision in detecting small targets and complex backgrounds. Secondly, we design a modified YOLOv7 global information DP-MLP module to effectively capture and integrate global information, thereby improving target detection accuracy and robustness, especially in handling large-scale variations and complex scenes. Lastly, we explore a semi-supervised learning model (SSLM) target detection algorithm incorporating unlabeled data, leveraging information from unlabeled data to enhance the model's generalization ability and performance. Experimental results demonstrate that despite the outstanding performance of YOLOv7, the mean average precision (MAP) can still be improved by 1.9%. Specifically, under testing on the TGRS-HRRSD-Dataset, the MFE and DP-MLP models achieve MAP values of 93.4% and 93.1%, respectively. Across the NWPU VHR-10 dataset, the three models achieve MAP values of 93.1%, 92.1%, and 92.2%, respectively. Significant improvements are observed across various metrics compared to the original model. This study enhances the adaptability, accuracy, and generalization of remote sensing image object detection.

MSA-Net: A Precise and Robust Model for Predicting the Carbon Content on an As-Received Basis of Coal.

The carbon content as received (Car) of coal is essential for the emission factor method in IPCC methodology. The traditional carbon measurement mechanism relies on detection equipment, resulting in significant detection costs. To reduce detection costs and provide precise predictions of Cars even in the absence of measurements, this paper proposes a neural network combining MLP with an attention mechanism (MSA-Net). In this model, the Attention Module is proposed to extract important and potential features. The Skip-Connections are utilized for feature reuse. The Huber loss is used to reduce the error between predicted Car values and actual values. The experimental results show that when the input includes eight measured parameters, the MAPE of MSA-Net is only 0.83%, which is better than the state-of-the-art Gaussian Process Regression (GPR) method. MSA-Net exhibits better predictive performance compared to MLP, RNN, LSTM, and Transformer. Moreover, this article provides two measurement solutions for thermal power enterprises to reduce detection costs.

Fabrication of a Capacitive 3D Spacer Fabric Pressure Sensor with a Dielectric Constant Change for High Sensitivity.

Smart wearable sensors are increasingly integrated into everyday life, interfacing with the human body to enable real-time monitoring of biological signals. This study focuses on creating high-sensitivity capacitive-type sensors by impregnating polyester-based 3D spacer fabric with a Carbon Nanotube (CNT) dispersion. The unique properties of conductive particles lead to nonlinear variations in the dielectric constant when pressure is applied, consequently affecting the gauge factor. The results reveal that while the fabric without CNT particles had a gauge factor of 1.967, the inclusion of 0.04 wt% CNT increased it significantly to 5.210. As sensor sensitivity requirements vary according to the application, identifying the necessary CNT wt% is crucial. Artificial intelligence, particularly the Multilayer Perception (MLP) model, enables nonlinear regression analysis for this purpose. The MLP model created and validated in this research showed a high correlation coefficient of 0.99564 between the model predictions and actual target values, indicating its effectiveness and reliability.

Diagnosis of Covid-19 from CT slices using Whale Optimization Algorithm, Support Vector Machine and Multi-Layer Perceptron.

BACKGROUND: The coronavirus disease 2019 is a serious and highly contagious disease caused by infection with a newly discovered virus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). OBJECTIVE: A Computer Aided Diagnosis (CAD) system to assist physicians to diagnose Covid-19 from chest Computed Tomography (CT) slices is modelled and experimented. METHODS: The lung tissues are segmented using Otsu's thresholding method. The Covid-19 lesions have been annotated as the Regions of Interest (ROIs), which is followed by texture and shape extraction. The obtained features are stored as feature vectors and split into 80:20 train and test sets. To choose the optimal features, Whale Optimization Algorithm (WOA) with Support Vector Machine (SVM) classifier's accuracy is employed. A Multi-Layer Perceptron (MLP) classifier is trained to perform classification with the selected features. RESULTS: Comparative experimentations of the proposed system with existing eight benchmark Machine Learning classifiers using real-time dataset demonstrates that the proposed system with 88.94% accuracy outperforms the benchmark classifier's results. Statistical analysis namely, Friedman test, Mann Whitney U test and Kendall's Rank Correlation Coefficient Test has been performed which indicates that the proposed method has a significant impact on the novel dataset considered. CONCLUSION: The MLP classifier's accuracy without feature selection yielded 80.40%, whereas with feature selection using WOA, it yielded 88.94%.

Landscape transition-induced ecological risk modeling using GIS and remote sensing techniques: a case of Saint Martin Island, Bangladesh.

Uncontrolled human activity and nature are causing the deterioration of Saint Martin Island, Bangladesh's only tropical island, necessitating sustainable land use strategies and ecological practices. Therefore, the present study measures the land use/cover transition from 1974 to 2021, predicts 2032 and 2042, and constructs the spatiotemporal features of the Landscape Ecological Risk Index based on land use changes. The study utilized Maximum Likelihood Classification (MLC) on Landsat images from 1974, 1988, 2001, 2013, and Sentinel 2B in 2021, achieving ≥ 80% accuracy. The MLP-MC approach was also used to predict 2032 and 2042 LULC change patterns. The eco-risk index was developed using landscape disturbance and vulnerability indices, Bayesian Kriging interpolation, and spatial autocorrelations to indicate spatial clustering. The research found that settlements increased from 2.06 to 28.62 ha between 1974 and 2021 and would cover 41.22 ha in 2042, causing considerable losses in agricultural areas, waterbodies, sand, coral reefs, and vegetation. The area under study showed a more uniform and homogenous environment as Shannon's diversity and evenness scores decreased. The ecological risk of Saint Martin Island increased from 4.31 to 31.05 ha between 1974 and 2042 due to natural and human factors like erosion, tidal bores, population growth, coral mining, habitat destruction, and intensive agricultural practices and tourism, primarily in Nazrul Para, Galachipa, and Western Dakhin Para. The findings will benefit St. Martin Island stakeholders and policymakers by providing insights into current and potential landscape changes and land eco-management.

PIS-Net: Efficient Medical Image Segmentation Network with Multivariate Downsampling for Point-of-Care.

Recently, with more portable diagnostic devices being moved to people anywhere, point-of-care (PoC) imaging has become more convenient and more popular than the traditional "bed imaging". Instant image segmentation, as an important technology of computer vision, is receiving more and more attention in PoC diagnosis. However, the image distortion caused by image preprocessing and the low resolution of medical images extracted by PoC devices are urgent problems that need to be solved. Moreover, more efficient feature representation is necessary in the design of instant image segmentation. In this paper, a new feature representation considering the relationships among local features with minimal parameters and a lower computational complexity is proposed. Since a feature window sliding along a diagonal can capture more pluralistic features, a Diagonal-Axial Multi-Layer Perceptron is designed to obtain the global correlation among local features for a more comprehensive feature representation. Additionally, a new multi-scale feature fusion is proposed to integrate nonlinear features with linear ones to obtain a more precise feature representation. Richer features are figured out. In order to improve the generalization of the models, a dynamic residual spatial pyramid pooling based on various receptive fields is constructed according to different sizes of images, which alleviates the influence of image distortion. The experimental results show that the proposed strategy has better performance on instant image segmentation. Notably, it yields an average improvement of 1.31% in Dice than existing strategies on the BUSI, ISIC2018 and MoNuSeg datasets.

Proteomics analysis of a tobacco variety resistant to brown spot disease and functional characterization of NbMLP423 in Nicotiana benthamiana.

BACKGROUND: Tobacco brown spot disease is an important disease caused by Alternaria alternata that affects tobacco production and quality worldwide. Planting resistant varieties is the most economical and effective way to control this disease. However, the lack of understanding of the mechanism of tobacco resistance to tobacco brown spot has hindered progress in the breeding of resistant varieties. METHODS AND RESULTS: In this study, differentially expressed proteins (DEPs), including 12 up-regulated and 11 down-regulated proteins, were screened using isobaric tags for relative and absolute quantification (iTRAQ) by comparing resistant and susceptible pools and analyzing the associated functions and metabolic pathways. Significantly up-regulated expression of the major latex-like protein gene 423 (MLP 423) was detected in both the resistant parent and the population pool. Bioinformatics analysis showed that the NbMLP423 cloned in Nicotiana benthamiana had a similar structure to the NtMLP423 in Nicotiana tabacum, and that expression of both genes respond rapidly to Alternaria alternata infection. NbMLP423 was then used to study the subcellular localization and expression in different tissues, followed by both silencing and the construction of an overexpression system for NbMLP423. The silenced plants demonstrated inhibited TBS resistance, while the overexpressed plants exhibited significantly enhanced resistance. Exogenous applications of plant hormones, such as salicylic acid, had a significant inducing effect on NbMLP423 expression. CONCLUSIONS: Taken together, our results provide insights into the role of NbMLP423 in plants against tobacco brown spot infection and provide a foundation for obtaining resistant tobacco varieties through the construction of new candidate genes of the MLP subfamily.

MLP-mmWP: High-Precision Millimeter Wave Positioning Based on MLP-Mixer Neural Networks.

Millimeter wave (MMW) communication, noted for its merit of wide bandwidth and high-speed transmission, is also a competitive implementation of the Internet of Everything (IoE). In an always-connected world, mutual data transmission and localization are the primary issues, such as the application of MMW application in autonomous vehicles and intelligent robots. Recently, artificial intelligence technologies have been adopted for the issues in the MMW communication domain. In this paper, MLP-mmWP, a deep learning method, is proposed to localize the user with respect to MMW communication information. The proposed method employs seven sequences of beamformed fingerprints (BFFs) to estimate localization, which includes line-of-sight (LOS) and non-line-of-sight (NLOS) transmissions. As far as we know, MLP-mmWP is the first method to apply the MLP-Mixer neural network to the task of MMW positioning. Moreover, experimental results in a public dataset demonstrate that MLP-mmWP outperforms the existing state-of-the-art methods. Specifically, in a simulation area of 400 × 400 m2, the positioning mean absolute error is 1.78 m, and the 95th percentile prediction error is 3.96 m, representing improvements of 11.8% and 8.2%, respectively.

Transfer Learning for Image-Based Malware Detection for IoT.

The tremendous growth in online activity and the Internet of Things (IoT) led to an increase in cyberattacks. Malware infiltrated at least one device in almost every household. Various malware detection methods that use shallow or deep IoT techniques were discovered in recent years. Deep learning models with a visualization method are the most commonly and popularly used strategy in most works. This method has the benefit of automatically extracting features, requiring less technical expertise, and using fewer resources during data processing. Training deep learning models that generalize effectively without overfitting is not feasible or appropriate with large datasets and complex architectures. In this paper, a novel ensemble model, Stacked Ensemble-autoencoder, GRU, and MLP or SE-AGM, composed of three light-weight neural network models-autoencoder, GRU, and MLP-that is trained on the 25 essential and encoded extracted features of the benchmark MalImg dataset for classification was proposed. The GRU model was tested for its suitability in malware detection due to its lesser usage in this domain. The proposed model used a concise set of malware features for training and classifying the malware classes, which reduced the time and resource consumption in comparison to other existing models. The novelty lies in the stacked ensemble method where the output of one intermediate model works as input for the next model, thereby refining the features as compared to the general notion of an ensemble approach. Inspiration was drawn from earlier image-based malware detection works and transfer learning ideas. To extract features from the MalImg dataset, a CNN-based transfer learning model that was trained from scratch on domain data was used. Data augmentation was an important step in the image processing stage to investigate its effect on classifying grayscale malware images in the MalImg dataset. SE-AGM outperformed existing approaches on the benchmark MalImg dataset with an average accuracy of 99.43%, demonstrating that our method was on par with or even surpassed them.

Wheel Defect Detection Using a Hybrid Deep Learning Approach.

Defective wheels pose a significant challenge in railway transportation, impacting operational performance and safety. Excessive traction and braking forces give rise to deviations from the intended conical tread shape, resulting in amplified vibrations and noise. Moreover, these deviations contribute to the accelerated damage of track components. Detecting wheel defects at an early stage is crucial to ensure safe and comfortable operation, as well as to minimize maintenance costs. However, the presence of various vibrations, such as those induced by the track, traction motors, and other rolling stock subsystems, poses a significant challenge for onboard detection techniques. These vibrations create difficulties in accurately identifying wheel defects in real-time during operational activities, often resulting in false alarms. This research paper aims to address this issue by using a hybrid deep learning-based approach for the accurate detection of various types of wheel defects using accelerometer data. The proposed approach aims to enhance wheel defect detection accuracy while considering onboard techniques' cost-effectiveness and efficiency. A realistic simulation model of the railway wheelset is developed to generate a comprehensive dataset. To generate vibration data in various scenarios, the model is simulated for 20 s under different conditions, including one non-faulty scenario and six faulty scenarios. The simulations are conducted at different speeds and track conditions to capture a wide range of operating conditions. Within each simulation iteration, a total of 200,000 data points are generated, providing a comprehensive dataset for analysis and evaluation. The generated data are then utilized to train and evaluate a hybrid deep learning model, employing a multi-layer perceptron (MLP) as a feature extractor and multiple machine learning models (support vector machine, random forest, decision tree, and k-nearest neighbors) for performance comparison. The results demonstrate that the MLP-RF (multi-layer perceptron with random forest) model achieved an accuracy of 99%, while the MLP-DT (multi-layer perceptron with decision tree) model achieved an accuracy of 98%. These high accuracy values indicate the effectiveness of the models in accurately classifying and predicting the outcomes. The contributions of this research work include the development of a realistic simulation model, the evaluation of sensor layout effectiveness, and the application of deep learning techniques for improved wheel flat detections.

A Deep Learning Model for Correlation Analysis between Electroencephalography Signal and Speech Stimuli.

In recent years, the use of electroencephalography (EEG) has grown as a tool for diagnostic and brain function monitoring, being a simple and non-invasive method compared with other procedures like histological sampling. Typically, in order to extract functional brain responses from EEG signals, prolonged and repeated stimuli are needed because of the artifacts generated in recordings which adversely impact the stimulus-response analysis. To mitigate the artifact effect, correlation analysis (CA) methods are applied in the literature, where the predominant approaches focus on enhancing stimulus-response correlations through the use of linear analysis methods like canonical correlation analysis (CCA). This paper introduces a novel CA framework based on a neural network with a loss function specifically designed to maximize correlation between EEG and speech stimuli. Compared with other deep learning CA approaches (DCCAs) in the literature, this framework introduces a single multilayer perceptron (MLP) network instead of two networks for each stimulus. To validate the proposed approach, a comparison with linear CCA (LCCA) and DCCA was performed, using a dataset containing the EEG traces of subjects listening to speech stimuli. The experimental results show that the proposed method improves the overall Pearson correlation by 10.56% compared with the state-of-the-art DCCA method.

Methodology for Creating a Digital Bathymetric Model Using Neural Networks for Combined Hydroacoustic and Photogrammetric Data in Shallow Water Areas.

This study uses a neural network to propose a methodology for creating digital bathymetric models for shallow water areas that are partially covered by a mix of hydroacoustic and photogrammetric data. A key challenge of this approach is the preparation of the training dataset from such data. Focusing on cases in which the training dataset covers only part of the measured depths, the approach employs generalized linear regression for data optimization followed by multilayer perceptron neural networks for bathymetric model creation. The research assessed the impact of data reduction, outlier elimination, and regression surface-based filtering on neural network learning. The average values of the root mean square (RMS) error were successively obtained for the studied nearshore, middle, and deep water areas, which were 0.12 m, 0.03 m, and 0.06 m, respectively; moreover, the values of the mean absolute error (MAE) were 0.11 m, 0.02 m, and 0.04 m, respectively. Following detailed quantitative and qualitative error analyses, the results indicate variable accuracy across different study areas. Nonetheless, the methodology demonstrated effectiveness in depth calculations for water bodies, although it faces challenges with respect to accuracy, especially in preserving nearshore values in shallow areas.

Genome-Wide Evolutionary Characterization and Expression Analysis of Major Latex Protein (MLP) Family Genes in Tomato.

Major latex proteins (MLPs) play a key role in plant response to abiotic and biotic stresses. However, little is known about this gene family in tomatoes (Solanum lycopersicum). In this paper, we perform a genome-wide evolutionary characterization and gene expression analysis of the MLP family in tomatoes. We found a total of 34 SlMLP members in the tomato genome, which are heterogeneously distributed on eight chromosomes. The phylogenetic analysis of the SlMLP family unveiled their evolutionary relationships and possible functions. Furthermore, the tissue-specific expression analysis revealed that the tomato MLP members possess distinct biological functions. Crucially, multiple cis-regulatory elements associated with stress, hormone, light, and growth responses were identified in the promoter regions of these SlMLP genes, suggesting that SlMLPs are potentially involved in plant growth, development, and various stress responses. Subcellular localization demonstrated that SlMLP1, SlMLP3, and SlMLP17 are localized in the cytoplasm. In conclusion, these findings lay a foundation for further dissecting the functions of tomato SlMLP genes and exploring the evolutionary relationships of MLP homologs in different plants.

Machine Learning-Enabled NIR Spectroscopy. Part 2: Workflow for Selecting a Subset of Samples from Publicly Accessible Data.

An increasingly large dataset of pharmaceutics disciplines is frequently challenging to comprehend. Since machine learning needs high-quality data sets, the open-source dataset can be a place to start. This work presents a systematic method to choose representative subsamples from the existing research, along with an extensive set of quality measures and a visualization strategy. The preceding article (Muthudoss et al.. in AAPS PharmSciTech 23, 2022) describes a workflow for leveraging near infrared (NIR) spectroscopy to obtain reliable and robust data on pharmaceutical samples. This study describes the systematic and structured procedure for selecting subsamples from the historical data. We offer a wide range of in-depth quality measures, diagnostic tools, and visualization techniques. A real-world, well-researched NIR dataset was employed to demonstrate this approach. This open-source tablet dataset ( http://www.models.life.ku.dk/Tablets ) consists of different doses in milligrams, different shapes, and sizes of dosage forms, slots in tablets, three different manufacturing scales (lab, pilot, production), coating differences (coated vs uncoated), etc. This sample is appropriate; that is, the model was developed on one scale (in this research, the lab scale), and it can be great to investigate how well the top models are transferable when tested on new data like pilot-scale or production (full) scale. A literature review indicated that the PLS regression models outperform artificial neural network-multilayer perceptron (ANN-MLP). This work demonstrates the selection of appropriate hyperparameters and their impact on ANN-MLP model performance. The hyperparameter tuning approaches and performance with available references are discussed for the data under investigation. Model extension from lab-scale to pilot-scale/production scale is demonstrated. HIGHLIGHTS: • We present a comprehensive quality metrics and visualization strategy in selecting subsamples from the existing studies • A comprehensive assessment and workflow are demonstrated using historical real-world near-infrared (NIR) data sets • Selection of appropriate hyperparameters and their impact on artificial neural network-multilayer perceptron (ANN-MLP) model performance • The choice of hyperparameter tuning approaches and performance with available references are discussed for the data under investigation • Model extension from lab-scale to pilot-scale successfully demonstrated.