Plant Phenomics. 2024 Mar 28;6:0159. doi: 10.34133/plantphenomics.0159. eCollection 2024.

ABSTRACT

The root is an important organ for plants to obtain nutrients and water, and its phenotypic characteristics are closely related to its functions. Deep-learning-based high-throughput in situ root senescence feature extraction has not yet been published. In light of this, this paper suggests a technique based on the transformer neural network for retrieving cotton's in situ root senescence properties. High-resolution in situ root pictures with various levels of senescence are the main subject of the investigation. By comparing the semantic segmentation of the root system by general convolutional neural networks and transformer neural networks, SegFormer-UN (large) achieves the optimal evaluation metrics with mIoU, mRecall, mPrecision, and mF1 metric values of 81.52%, 86.87%, 90.98%, and 88.81%, respectively. The segmentation results indicate more accurate predictions at the connections of root systems in the segmented images. In contrast to 2 algorithms for cotton root senescence extraction based on deep learning and image processing, the in situ root senescence recognition algorithm using the SegFormer-UN model has a parameter count of 5.81 million and operates at a fast speed, approximately 4 min per image. It can accurately identify senescence roots in the image. We propose that the SegFormer-UN model can rapidly and nondestructively identify senescence root in in situ root images, providing important methodological support for efficient crop senescence research.

PMID:38629083 | PMC:PMC11018523 | DOI:10.34133/plantphenomics.0159

Plant Phenomics. 2024 Apr 12;6:0175. doi: 10.34133/plantphenomics.0175. eCollection 2024.

ABSTRACT

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train) and error-prone (derived geometric features are sensitive to instance mask integrity). Here, we present a segmentation-free approach that leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that pose-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.

PMID:38629082 | PMC:PMC11020144 | DOI:10.34133/plantphenomics.0175

Plant Phenomics. 2024 Apr 15;6:0172. doi: 10.34133/plantphenomics.0172. eCollection 2024.

ABSTRACT

The number of flowers is essential for evaluating the growth status of litchi trees and enables researchers to estimate flowering rates and conduct various phenotypic studies, particularly focusing on the information of individual panicles. However, manual counting remains the primary method for quantifying flowers, and there has been insufficient emphasis on the advancement of reliable deep learning methods for estimation and their integration into research. Furthermore, the current density map-based methods are susceptible to background interference. To tackle the challenges of accurately quantifying small and dense male litchi flowers, a framework counting the flowers in panicles is proposed. Firstly, an existing effective algorithm YOLACT++ is utilized to segment individual panicles from images. Secondly, a novel algorithm FlowerNet based on density map regression is proposed to accurately count flowers in each panicle. By employing a multitask learning approach, FlowerNet effectively captures both foreground and background information, thereby overcoming interference from non-target areas during pixel-level regression tasks. It achieves a mean absolute error of 47.71 and a root mean squared error of 61.78 on the flower dataset constructed. Additionally, a regression equation is established using a dataset of inflorescences to examine the application of the algorithm for flower counting. It captures the relationship between the predicted number of flowers by FlowerNet and the manually counted number, resulting in a determination coefficient (R2) of 0.81. The proposed algorithm shows promise for automated estimation of litchi flowering quantity and can serve as a valuable reference for litchi orchard management during flowering period.

PMID:38629081 | PMC:PMC11018488 | DOI:10.34133/plantphenomics.0172

Plant Phenomics. 2024 Apr 15;6:0174. doi: 10.34133/plantphenomics.0174. eCollection 2024.

ABSTRACT

The deployment of intelligent surveillance systems to monitor tomato plant growth poses substantial challenges due to the dynamic nature of disease patterns and the complexity of environmental conditions such as background and lighting. In this study, an integrated cascade framework that synergizes detectors and trackers was introduced for the simultaneous identification of tomato leaf diseases and fruit counting. We applied an autonomous robot with smartphone camera to collect images for leaf disease and fruits in greenhouses. Further, we improved the deep learning network YOLO-TGI by incorporating Ghost and CBAM modules, which was trained and tested in conjunction with premier lightweight detection models like YOLOX and NanoDet in evaluating leaf health conditions. For the cascading with various base detectors, we integrated state-of-the-art trackers such as Byte-Track, Motpy, and FairMot to enable fruit counting in video streams. Experimental results indicated that the combination of YOLO-TGI and Byte-Track achieved the most robust performance. Particularly, YOLO-TGI-N emerged as the model with the least computational demands, registering the lowest FLOPs at 2.05 G and checkpoint weights at 3.7 M, while still maintaining a mAP of 0.72 for leaf disease detection. Regarding the fruit counting, the combination of YOLO-TGI-S and Byte-Track achieved the best R2 of 0.93 and the lowest RMSE of 9.17, boasting an inference speed that doubles that of the YOLOX series, and is 2.5 times faster than the NanoDet series. The developed network framework is a potential solution for researchers facilitating the deployment of similar surveillance models for a broad spectrum of fruit and vegetable crops.

PMID:38629080 | PMC:PMC11018486 | DOI:10.34133/plantphenomics.0174

iScience. 2024 Mar 29;27(5):109644. doi: 10.1016/j.isci.2024.109644. eCollection 2024 May 17.

ABSTRACT

While artificial intelligence drives remarkable progress in natural sciences, its broader societal implications are mostly disregarded. In this study, we evaluate environmental impacts of deep learning in materials science through extensive benchmarking. In particular, a set of diverse neural networks is trained for a given supervised learning task to assess greenhouse gas (GHG) emissions during training and inference phases. A chronological perspective showed diminishing returns, manifesting themselves as a 28% decrease in mean absolute error and nearly a 15,000% increase in the carbon footprint of model training in 2016-2022. By means of up-to-date graphics processing units, it is possible to partially offset the immense growth of GHG emissions. Nonetheless, the practice of employing energy-efficient hardware is overlooked by the materials informatics community, as follows from a literature analysis in the field. On the basis of our findings, we encourage researchers to report GHG emissions together with standard performance metrics.

PMID:38628964 | PMC:PMC11019266 | DOI:10.1016/j.isci.2024.109644

Front Med (Lausanne). 2024 Apr 2;11:1379211. doi: 10.3389/fmed.2024.1379211. eCollection 2024.

ABSTRACT

Integrating healthcare into traffic accident prevention through predictive modeling holds immense potential. Decentralized Defense presents a transformative vision for combating cyberbullying, prioritizing user privacy, fostering a safer online environment, and offering valuable insights for both healthcare and predictive modeling applications. As cyberbullying proliferates in social media, a pressing need exists for a robust and innovative solution that ensures user safety in the cyberspace. This paper aims toward introducing the approach of merging Blockchain and Federated Learning (FL), to create a decentralized AI solutions for cyberbullying. It has also used Alloy Language for formal modeling of social connections using specific declarations that are defined by the novel algorithm in the paper on two different datasets on Cyberbullying and are available online. The proposed novel method uses DBN to run established relation tests amongst the features in two phases, the first is LSTM to run tests to develop established features for the DBN layer and second is that these are run on various blocks of information of the blockchain. The performance of our proposed research is compared with the previous research and are evaluated using several metrics on creating the standard benchmarks for real world applications.

PMID:38628805 | PMC:PMC11020079 | DOI:10.3389/fmed.2024.1379211

Heliyon. 2024 Apr 4;10(8):e29077. doi: 10.1016/j.heliyon.2024.e29077. eCollection 2024 Apr 30.

ABSTRACT

Refined volatile organic compound (VOC) emission characteristics are crucial for accurate source apportionment in chemical industrial parks. The data from mobile monitoring platforms in chemical industrial parks contain pollution information that is not intuitively displayed, requiring further excavation. A novel approach was proposed to identify VOC emission characteristics using the class activation map (CAM) technology of convolutional neural network (CNN), which was applied on the mobile monitoring platform data (MD) derived from a typical fine chemical industrial park. It converts a large amount of monitoring data with high spatiotemporal complexity into simple and interpretable characteristic maps, effectively improving the identification effect of VOC emission characteristics, supporting more accurate source apportionment of VOC pollution around the park. Using this method, the VOC emission characteristics of eight key factories were identified. VOC source apportionment in the park was conducted for one day using a positive matrix factorization (PMF) model and seven combined factor profiles (CFPs) were calculated. Based on the identified VOC emission characteristics, the main pollution sources and their contributions to surrounding schools and residential areas were determined, revealing that one pesticide factory (named LKA) had the highest contribution ratio. The source apportionment results indicated that the impact of the chemical industrial park on the surrounding areas varied from morning to afternoon, which to some extent reflected the intermittent production methods employed for fine chemicals.

PMID:38628757 | PMC:PMC11019163 | DOI:10.1016/j.heliyon.2024.e29077

Heliyon. 2024 Apr 9;10(8):e28688. doi: 10.1016/j.heliyon.2024.e28688. eCollection 2024 Apr 30.

ABSTRACT

Elderly falls are a major concerning threat resulting in over 1.5-2 million elderly people experiencing severe injuries and 1 million deaths yearly. Falls experienced by Elderly people may lead to a long-term negative impact on their physical and psychological health conditions. Major healthcare research had focused on this lately to detect and prevent the fall. In this work, an Artificial Intelligence (AI) edge computing based wearable device is designed and developed for detection and prevention of fall of elderly people. Further, the various deep learning algorithms such as Convolutional Neural Network (CNN), Recurrent Neural Network (RNN), Long Short-Term Memory (LSTM), Gated Recurrent Unit (GRU) are utilized for activity recognition of elderly. Also, the CNN-LSTM, RNN-LSTM and GRU-LSTM with and without attention layer respectively are utilized and the performance metrics are analyzed to find the best deep learning model. Furthermore, the three different hardware boards such as Jetson Nano developer board, Raspberry PI 3 and 4 are utilized as an AI edge computing device and the best deep learning model is implemented and the computation time is evaluated. Results demonstrate that the CNN-LSTM with attention layer exhibits the accuracy, recall, precision and F1_Score of 97%, 98%, 98% and 0.98 respectively which is better when compared to other deep learning models. Also, the computation time of NVIDIA Jetson Nano is less when compared to other edge computing devices. This work appears to be of high societal relevance since the proposed wearable device can be used to monitor the activity of elderly and prevents the elderly falls which improve the quality of life of elderly people.

PMID:38628753 | PMC:PMC11019185 | DOI:10.1016/j.heliyon.2024.e28688

Heliyon. 2024 Apr 3;10(8):e29021. doi: 10.1016/j.heliyon.2024.e29021. eCollection 2024 Apr 30.

ABSTRACT

With the rapid development of the national economy, power security is very important for the security of the country and people's happiness. Electricity is an important energy source for a country. Even if the power system malfunctions for a short period of time, it would cause incalculable losses to social production and people's lives. Among them, one of the most important reasons for power system faults is the occurrence of power line faults, so diagnosing faulty lines has great research significance. On the basis of analyzing the structure and working principle of the deep learning model convolutional neural network (CNN), this article used the CNN model to diagnose faults in power lines and analyzed the simulation results. It was found that different CNN structures have different fault diagnosis accuracy for power lines. The fewer the number of batches in the network structure and the more the number of training sessions, the higher its fault determination accuracy. In the power line fault diagnosis based on three deep learning algorithms, the CNN has the highest stable fault diagnosis accuracy of 100%; the recursive neural network has the second stable fault diagnosis accuracy of 93.4%; the deep belief network has the lowest stable fault diagnosis accuracy of 91.5%. In the comparison of power line fault diagnosis stability, the accuracy standard deviation of CNN is close to 0, and they are also the most stable in power circuit fault diagnosis. The stability of algorithmic recurrent neural networks is between the two, and the accuracy standard deviation of deep belief networks is 1.84% when trained 12 times. Their fault diagnosis stability is also the worst.

PMID:38628723 | PMC:PMC11019159 | DOI:10.1016/j.heliyon.2024.e29021

Cancer Imaging. 2024 Apr 16;24(1):52. doi: 10.1186/s40644-024-00697-5.

ABSTRACT

BACKGROUND: Combining conventional radiomics models with deep learning features can result in superior performance in predicting the prognosis of patients with tumors; however, this approach has never been evaluated for the prediction of metachronous distant metastasis (MDM) among patients with retroperitoneal leiomyosarcoma (RLS). Thus, the purpose of this study was to develop and validate a preoperative contrast-enhanced computed tomography (CECT)-based deep learning radiomics model for predicting the occurrence of MDM in patients with RLS undergoing complete surgical resection.

METHODS: A total of 179 patients who had undergone surgery for the treatment of histologically confirmed RLS were retrospectively recruited from two tertiary sarcoma centers. Semantic segmentation features derived from a convolutional neural network deep learning model as well as conventional hand-crafted radiomics features were extracted from preoperative three-phase CECT images to quantify the sarcoma phenotypes. A conventional radiomics signature (RS) and a deep learning radiomics signature (DLRS) that incorporated hand-crafted radiomics and deep learning features were developed to predict the risk of MDM. Additionally, a deep learning radiomics nomogram (DLRN) was established to evaluate the incremental prognostic significance of the DLRS in combination with clinico-radiological predictors.

RESULTS: The comparison of the area under the curve (AUC) values in the external validation set, as determined by the DeLong test, demonstrated that the integrated DLRN, DLRS, and RS models all exhibited superior predictive performance compared with that of the clinical model (AUC 0.786 [95% confidence interval 0.649-0.923] vs. 0.822 [0.692-0.952] vs. 0.733 [0.573-0.892] vs. 0.511 [0.359-0.662]; both P < 0.05). The decision curve analyses graphically indicated that utilizing the DLRN for risk stratification provided greater net benefits than those achieved using the DLRS, RS and clinical models. Good alignment with the calibration curve indicated that the DLRN also exhibited good performance.

CONCLUSIONS: The novel CECT-based DLRN developed in this study demonstrated promising performance in the preoperative prediction of the risk of MDM following curative resection in patients with RLS. The DLRN, which outperformed the other three models, could provide valuable information for predicting surgical efficacy and tailoring individualized treatment plans in this patient population.

TRIAL REGISTRATION: Not applicable.

PMID:38627828 | DOI:10.1186/s40644-024-00697-5

BMC Med Imaging. 2024 Apr 16;24(1):91. doi: 10.1186/s12880-024-01255-y.

ABSTRACT

BACKGROUND: The relationship between the biological pathways related to deep learning radiomics (DLR) and lymph node metastasis (LNM) of breast cancer is still poorly understood. This study explored the value of DLR based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in LNM of invasive breast cancer. It also analyzed the biological significance of DLR phenotype based on genomics.

METHODS: Two cohorts from the Cancer Imaging Archive project were used, one as the training cohort (TCGA-Breast, n = 88) and one as the validation cohort (Breast-MRI-NACT Pilot, n = 57). Radiomics and deep learning features were extracted from preoperative DCE-MRI. After dual selection by principal components analysis (PCA) and relief methods, radiomics and deep learning models for predicting LNM were constructed by the random forest (RF) method. A post-fusion strategy was used to construct the DLR nomograms (DLRNs) for predicting LNM. The performance of the models was evaluated using the receiver operating characteristic (ROC) curve and Delong test. In the training cohort, transcriptome data were downloaded from the UCSC Xena online database, and biological pathways related to the DLR phenotypes were identified. Finally, hub genes were identified to obtain DLR gene expression (RadDeepGene) scores.

RESULTS: DLRNs were based on area under curve (AUC) evaluation (training cohort, AUC = 0.98; validation cohort, AUC = 0.87), which were higher than single radiomics models or GoogLeNet models. The Delong test (radiomics model, P = 0.04; GoogLeNet model, P = 0.01) also validated the above results in the training cohorts, but they were not statistically significant in the validation cohort. The GoogLeNet phenotypes were related to multiple classical tumor signaling pathways, characterizing the biological significance of immune response, signal transduction, and cell death. In all, 20 genes related to GoogLeNet phenotypes were identified, and the RadDeepGene score represented a high risk of LNM (odd ratio = 164.00, P < 0.001).

CONCLUSIONS: DLRNs combining radiomics and deep learning features of DCE-MRI images improved the preoperative prediction of LNM in breast cancer, and the potential biological characteristics of DLRN were identified through genomics.

PMID:38627678 | DOI:10.1186/s12880-024-01255-y

Nat Med. 2024 Apr 16. doi: 10.1038/s41591-024-02915-w. Online ahead of print.

ABSTRACT

Cancer of unknown primary (CUP) site poses diagnostic challenges due to its elusive nature. Many cases of CUP manifest as pleural and peritoneal serous effusions. Leveraging cytological images from 57,220 cases at four tertiary hospitals, we developed a deep-learning method for tumor origin differentiation using cytological histology (TORCH) that can identify malignancy and predict tumor origin in both hydrothorax and ascites. We examined its performance on three internal (n = 12,799) and two external (n = 14,538) testing sets. In both internal and external testing sets, TORCH achieved area under the receiver operating curve values ranging from 0.953 to 0.991 for cancer diagnosis and 0.953 to 0.979 for tumor origin localization. TORCH accurately predicted primary tumor origins, with a top-1 accuracy of 82.6% and top-3 accuracy of 98.9%. Compared with results derived from pathologists, TORCH showed better prediction efficacy (1.677 versus 1.265, P < 0.001), enhancing junior pathologists' diagnostic scores significantly (1.326 versus 1.101, P < 0.001). Patients with CUP whose initial treatment protocol was concordant with TORCH-predicted origins had better overall survival than those who were administrated discordant treatment (27 versus 17 months, P = 0.006). Our study underscores the potential of TORCH as a valuable ancillary tool in clinical practice, although further validation in randomized trials is warranted.

PMID:38627559 | DOI:10.1038/s41591-024-02915-w

World J Urol. 2024 Apr 16;42(1):238. doi: 10.1007/s00345-024-04921-6.

ABSTRACT

BACKGROUND: Accurate estimation of the glomerular filtration rate (GFR) is clinically crucial for determining the status of obstruction, developing treatment strategies, and predicting prognosis in obstructive nephropathy (ON). We aimed to develop a deep learning-based system, named UroAngel, for non-invasive and convenient prediction of single-kidney function level.

METHODS: We retrospectively collected computed tomography urography (CTU) images and emission computed tomography diagnostic reports of 520 ON patients. A 3D U-Net model was used to segment the renal parenchyma, and a logistic regression multi-classification model was used to predict renal function level. We compared the predictive performance of UroAngel with the Modification of Diet in Renal Disease (MDRD), Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations, and two expert radiologists in an additional 40 ON patients to validate clinical effectiveness.

RESULTS: UroAngel based on 3D U-Net convolutional neural network could segment the renal cortex accurately, with a Dice similarity coefficient of 0.861. Using the segmented renal cortex to predict renal function stage had high performance with an accuracy of 0.918, outperforming MDRD and CKD-EPI and two radiologists.

CONCLUSIONS: We proposed an automated 3D U-Net-based analysis system for direct prediction of single-kidney function stage from CTU images. UroAngel could accurately predict single-kidney function in ON patients, providing a novel, reliable, convenient, and non-invasive method.

PMID:38627315 | DOI:10.1007/s00345-024-04921-6

Eur Radiol. 2024 Apr 16. doi: 10.1007/s00330-024-10728-1. Online ahead of print.

ABSTRACT

OBJECTIVES: To build self-supervised foundation models for multicontrast MRI of the whole brain and evaluate their efficacy in assisting diagnosis of brain tumors.

METHODS: In this retrospective study, foundation models were developed using 57,621 enhanced head MRI scans through self-supervised learning with a pretext task of cross-contrast context restoration with two different content dropout schemes. Downstream classifiers were constructed based on the pretrained foundation models and fine-tuned for brain tumor detection, discrimination, and molecular status prediction. Metrics including accuracy, sensitivity, specificity, and area under the ROC curve (AUC) were used to evaluate the performance. Convolutional neural networks trained exclusively on downstream task data were employed for comparative analysis.

RESULTS: The pretrained foundation models demonstrated their ability to extract effective representations from multicontrast whole-brain volumes. The best classifiers, endowed with pretrained weights, showed remarkable performance with accuracies of 94.9, 92.3, and 80.4%, and corresponding AUC values of 0.981, 0.972, and 0.852 on independent test datasets in brain tumor detection, discrimination, and molecular status prediction, respectively. The classifiers with pretrained weights outperformed the convolutional classifiers trained from scratch by approximately 10% in terms of accuracy and AUC across all tasks. The saliency regions in the correctly predicted cases are mainly clustered around the tumors. Classifiers derived from the two dropout schemes differed significantly only in the detection of brain tumors.

CONCLUSIONS: Foundation models obtained from self-supervised learning have demonstrated encouraging potential for scalability and interpretability in downstream brain tumor-related tasks and hold promise for extension to neurological diseases with diffusely distributed lesions.

CLINICAL RELEVANCE STATEMENT: The application of our proposed method to the prediction of key molecular status in gliomas is expected to improve treatment planning and patient outcomes. Additionally, the foundation model we developed could serve as a cornerstone for advancing AI applications in the diagnosis of brain-related diseases.

PMID:38627290 | DOI:10.1007/s00330-024-10728-1

J Imaging Inform Med. 2024 Apr 16. doi: 10.1007/s10278-024-01085-y. Online ahead of print.

ABSTRACT

Architectural distortion (AD) is one of the most common findings on mammograms, and it may represent not only cancer but also a lesion such as a radial scar that may have an associated cancer. AD accounts for 18-45% missed cancer, and the positive predictive value of AD is approximately 74.5%. Early detection of AD leads to early diagnosis and treatment of the cancer and improves the overall prognosis. However, detection of AD is a challenging task. In this work, we propose a new approach for detecting architectural distortion in mammography images by combining preprocessing methods and a novel structure fusion attention model. The proposed structure-focused weighted orientation preprocessing method is composed of the original image, the architecture enhancement map, and the weighted orientation map, highlighting suspicious AD locations. The proposed structure fusion attention model captures the information from different channels and outperforms other models in terms of false positives and top sensitivity, which refers to the maximum sensitivity that a model can achieve under the acceptance of the highest number of false positives, reaching 0.92 top sensitivity with only 0.6590 false positive per image. The findings suggest that the combination of preprocessing methods and a novel network architecture can lead to more accurate and reliable AD detection. Overall, the proposed approach offers a novel perspective on detecting ADs, and we believe that our method can be applied to clinical settings in the future, assisting radiologists in the early detection of ADs from mammography, ultimately leading to early treatment of breast cancer patients.

PMID:38627268 | DOI:10.1007/s10278-024-01085-y

Sci Total Environ. 2024 Apr 14:172466. doi: 10.1016/j.scitotenv.2024.172466. Online ahead of print.

ABSTRACT

The burgeoning issue of plasmid-mediated resistance genes (ARGs) dissemination poses a significant threat to environmental integrity. However, the prediction of ARGs prevalence is overlooked, especially for emerging ARGs that are potentially evolving gene exchange hotspot. Here, we explored to classify plasmid or chromosome sequences and detect resistance gene prevalence by using DNABERT. Initially, the DNABERT fine-tuned in plasmid and chromosome sequences followed by multilayer perceptron (MLP) classifier could achieve 0.764 AUC (Area under curve) on external datasets across 23 genera, outperforming 0.02 AUC than traditional statistic-based model. Furthermore, Escherichia, Pseudomonas single genera based model were also be trained to explore its predict performance to ARGs prevalence detection. By integrating K-mer frequency attributes, our model could boost the performance to predict the prevalence of ARGs in an external dataset in Escherichia with 0.0281-0.0615 AUC and Pseudomonas with 0.0196-0.0928 AUC. Finally, we established a random forest model aimed at forecasting the relative conjugation transfer rate of plasmids with 0.7956 AUC, drawing on data from existing literature. It identifies the plasmid's repression status, cellular density, and temperature as the most important factors influencing transfer frequency. With these two models combined, they provide useful reference for quick and low-cost integrated evaluation of resistance gene transfer, accelerating the process of computer-assisted quantitative risk assessment of ARGs transfer in environmental field.

PMID:38626826 | DOI:10.1016/j.scitotenv.2024.172466

Biomed Mater. 2024 Apr 16. doi: 10.1088/1748-605X/ad3f60. Online ahead of print.

ABSTRACT

Accurate segmentation of coronary artery tree and personalised 3D printing from medical images is essential for CAD diagnosis and treatment. The current literature on 3D printing relies solely on generic models created with different software or 3D coronary artery models manually segmented from medical images. Moreover, there are not many studies examining the bioprintability of a 3D model generated by artificial intelligence (AI) segmentation for complex and branched structures. In this study, deep learning algorithms with transfer learning have been employed for accurate segmentation of the coronary artery tree from medical images to generate printable segmentations. We propose a combination of deep learning and 3D printing, which accurately segments and prints complex vascular patterns in coronary arteries. Then, we performed the 3D printing of the AI-generated coronary artery segmentation for the fabrication of bifurcated hollow vascular structure. Our results indicate improved performance of segmentation with the aid of transfer learning with a Dice overlap score of 0.86 on a test set of 10 CTA images. Then, bifurcated regions from 3D models were printed into the Pluronic F-127 support bath using alginate+glucomannan hydrogel. We successfully fabricated the bifurcated coronary artery structures with high length and wall thickness accuracy, however, the outer diameters of the vessels and length of the bifurcation point differ from the 3D models. The extrusion of unnecessary material, primarily observed when the nozzle moves from left to the right vessel during 3D printing, can be mitigated by adjusting the nozzle speed. Moreover, the shape accuracy can also be improved by designing a multi-axis printhead that can change the printing angle in three dimensions. Thus, this study demonstrates the potential of the use of AI-segmented 3D models in the 3D printing of coronary artery structures and, when further improved, can be used for the fabrication of patient-specific vascular implants.

PMID:38626778 | DOI:10.1088/1748-605X/ad3f60

Cell Rep Methods. 2024 Apr 10:100759. doi: 10.1016/j.crmeth.2024.100759. Online ahead of print.

ABSTRACT

We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole-slide image (WSI), optimized for patient-derived xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genome input and stand-alone image analysis. We show the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of H&E imaging features reveal similar patterns arising from the two data modalities.

PMID:38626768 | DOI:10.1016/j.crmeth.2024.100759

Spectrochim Acta A Mol Biomol Spectrosc. 2024 Apr 4;315:124251. doi: 10.1016/j.saa.2024.124251. Online ahead of print.

ABSTRACT

Uyghur medicine is one of the four major ethnic medicines in China and is a component of traditional Chinese medicine. The intrinsic quality of Uyghur medicinal materials will directly affect the clinical efficacy of Uyghur medicinal preparations. However, in recent years, problems such as adulteration of Uyghur medicinal materials and foreign bodies with the same name still exist, so it is necessary to strengthen the quality control of Uyghur medicines to guarantee Uyghur medicinal efficacy. Identifying the components of Uyghur medicines can clarify the types of medicinal materials used, is a crucial step to realizing the quality control of Uyghur medicines, and is also an important step in screening the effective components of Uyghur medicines. Currently, the method of identifying the components of Uyghur medicines relies on manual detection, which has the problems of high toxicity of the unfolding agent, poor stability, high cost, low efficiency, etc. Therefore, this paper proposes a method based on Raman spectroscopy and multi-label deep learning model to construct a model Mix2Com for accurate identification of Uyghur medicine components. The experiments use computer-simulated mixtures as the dataset, introduce the Long Short-Term Memory Model (LSTM) and Attention mechanism to encode the Raman spectral data, use multiple parallel networks for decoding, and ultimately realize the macro parallel prediction of medicine components. The results show that the model is trained to achieve 90.76% accuracy, 99.41% precision, 95.42% recall value and 97.37% F1 score. Compared to the traditional XGBoost model, the method proposed in the experiment improves the accuracy by 49% and the recall value by 18%; compared with the DeepRaman model, the accuracy is improved by 9% and the recall value is improved by 14%. The method proposed in this paper provides a new solution for the accurate identification of Uyghur medicinal components. It helps to improve the quality standard of Uyghur medicinal materials, advance the research on screening of effective chemical components of Uyghur medicines and their action mechanisms, and then promote the modernization and development of Uyghur medicine.

PMID:38626675 | DOI:10.1016/j.saa.2024.124251

Comput Med Imaging Graph. 2024 Apr 12;115:102380. doi: 10.1016/j.compmedimag.2024.102380. Online ahead of print.

ABSTRACT

The absence of bone wall located in the jugular bulb and sigmoid sinus of the temporal bone is one of the important reasons for pulsatile tinnitus. Automatic and accurate detection of these abnormal singes in CT slices has important theoretical significance and clinical value. Due to the shortage of abnormal samples, imbalanced samples, small inter-class differences, and low interpretability, existing deep-learning methods are greatly challenged. In this paper, we proposed a sub-features orthogonal decoupling model, which can effectively disentangle the representation features into class-specific sub-features and class-independent sub-features in a latent space. The former contains the discriminative information, while, the latter preserves information for image reconstruction. In addition, the proposed method can generate image samples using category conversion by combining the different class-specific sub-features and the class-independent sub-features, achieving corresponding mapping between deep features and images of specific classes. The proposed model improves the interpretability of the deep model and provides image synthesis methods for downstream tasks. The effectiveness of the method was verified in the detection of bone wall absence in the temporal bone jugular bulb and sigmoid sinus.

PMID:38626631 | DOI:10.1016/j.compmedimag.2024.102380