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1.
J Transl Med ; 22(1): 438, 2024 May 08.
Artículo en Inglés | MEDLINE | ID: mdl-38720336

RESUMEN

BACKGROUND: Advanced unresectable gastric cancer (GC) patients were previously treated with chemotherapy alone as the first-line therapy. However, with the Food and Drug Administration's (FDA) 2022 approval of programmed cell death protein 1 (PD-1) inhibitor combined with chemotherapy as the first-li ne treatment for advanced unresectable GC, patients have significantly benefited. However, the significant costs and potential adverse effects necessitate precise patient selection. In recent years, the advent of deep learning (DL) has revolutionized the medical field, particularly in predicting tumor treatment responses. Our study utilizes DL to analyze pathological images, aiming to predict first-line PD-1 combined chemotherapy response for advanced-stage GC. METHODS: In this multicenter retrospective analysis, Hematoxylin and Eosin (H&E)-stained slides were collected from advanced GC patients across four medical centers. Treatment response was evaluated according to iRECIST 1.1 criteria after a comprehensive first-line PD-1 immunotherapy combined with chemotherapy. Three DL models were employed in an ensemble approach to create the immune checkpoint inhibitors Response Score (ICIsRS) as a novel histopathological biomarker derived from Whole Slide Images (WSIs). RESULTS: Analyzing 148,181 patches from 313 WSIs of 264 advanced GC patients, the ensemble model exhibited superior predictive accuracy, leading to the creation of ICIsNet. The model demonstrated robust performance across four testing datasets, achieving AUC values of 0.92, 0.95, 0.96, and 1 respectively. The boxplot, constructed from the ICIsRS, reveals statistically significant disparities between the well response and poor response (all p-values < = 0.001). CONCLUSION: ICIsRS, a DL-derived biomarker from WSIs, effectively predicts advanced GC patients' responses to PD-1 combined chemotherapy, offering a novel approach for personalized treatment planning and allowing for more individualized and potentially effective treatment strategies based on a patient's unique response situations.


Asunto(s)
Aprendizaje Profundo , Inhibidores de Puntos de Control Inmunológico , Receptor de Muerte Celular Programada 1 , Neoplasias Gástricas , Humanos , Neoplasias Gástricas/tratamiento farmacológico , Neoplasias Gástricas/patología , Masculino , Femenino , Resultado del Tratamiento , Persona de Mediana Edad , Inhibidores de Puntos de Control Inmunológico/uso terapéutico , Receptor de Muerte Celular Programada 1/antagonistas & inhibidores , Anciano , Estudios Retrospectivos , Curva ROC , Adulto
2.
J Transl Med ; 22(1): 434, 2024 May 08.
Artículo en Inglés | MEDLINE | ID: mdl-38720370

RESUMEN

BACKGROUND: Cardiometabolic disorders pose significant health risks globally. Metabolic syndrome, characterized by a cluster of potentially reversible metabolic abnormalities, is a known risk factor for these disorders. Early detection and intervention for individuals with metabolic abnormalities can help mitigate the risk of developing more serious cardiometabolic conditions. This study aimed to develop an image-derived phenotype (IDP) for metabolic abnormality from unenhanced abdominal computed tomography (CT) scans using deep learning. We used this IDP to classify individuals with metabolic syndrome and predict future occurrence of cardiometabolic disorders. METHODS: A multi-stage deep learning approach was used to extract the IDP from the liver region of unenhanced abdominal CT scans. In a cohort of over 2,000 individuals the IDP was used to classify individuals with metabolic syndrome. In a subset of over 1,300 individuals, the IDP was used to predict future occurrence of hypertension, type II diabetes, and fatty liver disease. RESULTS: For metabolic syndrome (MetS) classification, we compared the performance of the proposed IDP to liver attenuation and visceral adipose tissue area (VAT). The proposed IDP showed the strongest performance (AUC 0.82) compared to attenuation (AUC 0.70) and VAT (AUC 0.80). For disease prediction, we compared the performance of the IDP to baseline MetS diagnosis. The models including the IDP outperformed MetS for type II diabetes (AUCs 0.91 and 0.90) and fatty liver disease (AUCs 0.67 and 0.62) prediction and performed comparably for hypertension prediction (AUCs of 0.77). CONCLUSIONS: This study demonstrated the superior performance of a deep learning IDP compared to traditional radiomic features to classify individuals with metabolic syndrome. Additionally, the IDP outperformed the clinical definition of metabolic syndrome in predicting future morbidities. Our findings underscore the utility of data-driven imaging phenotypes as valuable tools in the assessment and management of metabolic syndrome and cardiometabolic disorders.


Asunto(s)
Aprendizaje Profundo , Síndrome Metabólico , Fenotipo , Humanos , Síndrome Metabólico/diagnóstico por imagen , Síndrome Metabólico/complicaciones , Femenino , Masculino , Persona de Mediana Edad , Tomografía Computarizada por Rayos X , Enfermedades Cardiovasculares/diagnóstico por imagen , Adulto , Procesamiento de Imagen Asistido por Computador/métodos
3.
Cancer Imaging ; 24(1): 60, 2024 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-38720391

RESUMEN

BACKGROUND: This study systematically compares the impact of innovative deep learning image reconstruction (DLIR, TrueFidelity) to conventionally used iterative reconstruction (IR) on nodule volumetry and subjective image quality (IQ) at highly reduced radiation doses. This is essential in the context of low-dose CT lung cancer screening where accurate volumetry and characterization of pulmonary nodules in repeated CT scanning are indispensable. MATERIALS AND METHODS: A standardized CT dataset was established using an anthropomorphic chest phantom (Lungman, Kyoto Kaguku Inc., Kyoto, Japan) containing a set of 3D-printed lung nodules including six diameters (4 to 9 mm) and three morphology classes (lobular, spiculated, smooth), with an established ground truth. Images were acquired at varying radiation doses (6.04, 3.03, 1.54, 0.77, 0.41 and 0.20 mGy) and reconstructed with combinations of reconstruction kernels (soft and hard kernel) and reconstruction algorithms (ASIR-V and DLIR at low, medium and high strength). Semi-automatic volumetry measurements and subjective image quality scores recorded by five radiologists were analyzed with multiple linear regression and mixed-effect ordinal logistic regression models. RESULTS: Volumetric errors of nodules imaged with DLIR are up to 50% lower compared to ASIR-V, especially at radiation doses below 1 mGy and when reconstructed with a hard kernel. Also, across all nodule diameters and morphologies, volumetric errors are commonly lower with DLIR. Furthermore, DLIR renders higher subjective IQ, especially at the sub-mGy doses. Radiologists were up to nine times more likely to score the highest IQ-score to these images compared to those reconstructed with ASIR-V. Lung nodules with irregular margins and small diameters also had an increased likelihood (up to five times more likely) to be ascribed the best IQ scores when reconstructed with DLIR. CONCLUSION: We observed that DLIR performs as good as or even outperforms conventionally used reconstruction algorithms in terms of volumetric accuracy and subjective IQ of nodules in an anthropomorphic chest phantom. As such, DLIR potentially allows to lower the radiation dose to participants of lung cancer screening without compromising accurate measurement and characterization of lung nodules.


Asunto(s)
Aprendizaje Profundo , Neoplasias Pulmonares , Nódulos Pulmonares Múltiples , Fantasmas de Imagen , Dosis de Radiación , Tomografía Computarizada por Rayos X , Humanos , Tomografía Computarizada por Rayos X/métodos , Nódulos Pulmonares Múltiples/diagnóstico por imagen , Nódulos Pulmonares Múltiples/patología , Neoplasias Pulmonares/diagnóstico por imagen , Neoplasias Pulmonares/patología , Nódulo Pulmonar Solitario/diagnóstico por imagen , Nódulo Pulmonar Solitario/patología , Interpretación de Imagen Radiográfica Asistida por Computador/métodos , Procesamiento de Imagen Asistido por Computador/métodos
4.
Microbiome ; 12(1): 84, 2024 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-38725076

RESUMEN

BACKGROUND: Emergence of antibiotic resistance in bacteria is an important threat to global health. Antibiotic resistance genes (ARGs) are some of the key components to define bacterial resistance and their spread in different environments. Identification of ARGs, particularly from high-throughput sequencing data of the specimens, is the state-of-the-art method for comprehensively monitoring their spread and evolution. Current computational methods to identify ARGs mainly rely on alignment-based sequence similarities with known ARGs. Such approaches are limited by choice of reference databases and may potentially miss novel ARGs. The similarity thresholds are usually simple and could not accommodate variations across different gene families and regions. It is also difficult to scale up when sequence data are increasing. RESULTS: In this study, we developed ARGNet, a deep neural network that incorporates an unsupervised learning autoencoder model to identify ARGs and a multiclass classification convolutional neural network to classify ARGs that do not depend on sequence alignment. This approach enables a more efficient discovery of both known and novel ARGs. ARGNet accepts both amino acid and nucleotide sequences of variable lengths, from partial (30-50 aa; 100-150 nt) sequences to full-length protein or genes, allowing its application in both target sequencing and metagenomic sequencing. Our performance evaluation showed that ARGNet outperformed other deep learning models including DeepARG and HMD-ARG in most of the application scenarios especially quasi-negative test and the analysis of prediction consistency with phylogenetic tree. ARGNet has a reduced inference runtime by up to 57% relative to DeepARG. CONCLUSIONS: ARGNet is flexible, efficient, and accurate at predicting a broad range of ARGs from the sequencing data. ARGNet is freely available at https://github.com/id-bioinfo/ARGNet , with an online service provided at https://ARGNet.hku.hk . Video Abstract.


Asunto(s)
Bacterias , Redes Neurales de la Computación , Bacterias/genética , Bacterias/efectos de los fármacos , Bacterias/clasificación , Farmacorresistencia Bacteriana/genética , Antibacterianos/farmacología , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Biología Computacional/métodos , Genes Bacterianos/genética , Farmacorresistencia Microbiana/genética , Humanos , Aprendizaje Profundo
5.
F1000Res ; 13: 274, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38725640

RESUMEN

Background: The most recent advances in Computed Tomography (CT) image reconstruction technology are Deep learning image reconstruction (DLIR) algorithms. Due to drawbacks in Iterative reconstruction (IR) techniques such as negative image texture and nonlinear spatial resolutions, DLIRs are gradually replacing them. However, the potential use of DLIR in Head and Chest CT has to be examined further. Hence, the purpose of the study is to review the influence of DLIR on Radiation dose (RD), Image noise (IN), and outcomes of the studies compared with IR and FBP in Head and Chest CT examinations. Methods: We performed a detailed search in PubMed, Scopus, Web of Science, Cochrane Library, and Embase to find the articles reported using DLIR for Head and Chest CT examinations between 2017 to 2023. Data were retrieved from the short-listed studies using Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines. Results: Out of 196 articles searched, 15 articles were included. A total of 1292 sample size was included. 14 articles were rated as high and 1 article as moderate quality. All studies compared DLIR to IR techniques. 5 studies compared DLIR with IR and FBP. The review showed that DLIR improved IQ, and reduced RD and IN for CT Head and Chest examinations. Conclusions: DLIR algorithm have demonstrated a noted enhancement in IQ with reduced IN for CT Head and Chest examinations at lower dose compared with IR and FBP. DLIR showed potential for enhancing patient care by reducing radiation risks and increasing diagnostic accuracy.


Asunto(s)
Algoritmos , Aprendizaje Profundo , Cabeza , Dosis de Radiación , Tomografía Computarizada por Rayos X , Humanos , Tomografía Computarizada por Rayos X/métodos , Cabeza/diagnóstico por imagen , Procesamiento de Imagen Asistido por Computador/métodos , Tórax/diagnóstico por imagen , Radiografía Torácica/métodos , Relación Señal-Ruido
6.
PLoS One ; 19(5): e0300746, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38722916

RESUMEN

Wheat is a major grain crop in China, accounting for one-fifth of the national grain production. Drought stress severely affects the normal growth and development of wheat, leading to total crop failure, reduced yields, and quality. To address the lag and limitations inherent in traditional drought monitoring methods, this paper proposes a multimodal deep learning-based drought stress monitoring S-DNet model for winter wheat during its critical growth periods. Drought stress images of winter wheat during the Rise-Jointing, Heading-Flowering and Flowering-Maturity stages were acquired to establish a dataset corresponding to soil moisture monitoring data. The DenseNet-121 model was selected as the base network to extract drought features. Combining the drought phenotypic characteristics of wheat in the field with meteorological factors and IoT technology, the study integrated the meteorological drought index SPEI, based on WSN sensors, and deep image learning data to build a multimodal deep learning-based S-DNet model for monitoring drought stress in winter wheat. The results show that, compared to the single-modal DenseNet-121 model, the multimodal S-DNet model has higher robustness and generalization capability, with an average drought recognition accuracy reaching 96.4%. This effectively achieves non-destructive, accurate, and rapid monitoring of drought stress in winter wheat.


Asunto(s)
Aprendizaje Profundo , Sequías , Triticum , Triticum/crecimiento & desarrollo , Triticum/fisiología , Estaciones del Año , China , Estrés Fisiológico
7.
PLoS One ; 19(5): e0303519, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38723044

RESUMEN

OBJECTIVE: To establish whether or not a natural language processing technique could identify two common inpatient neurosurgical comorbidities using only text reports of inpatient head imaging. MATERIALS AND METHODS: A training and testing dataset of reports of 979 CT or MRI scans of the brain for patients admitted to the neurosurgery service of a single hospital in June 2021 or to the Emergency Department between July 1-8, 2021, was identified. A variety of machine learning and deep learning algorithms utilizing natural language processing were trained on the training set (84% of the total cohort) and tested on the remaining images. A subset comparison cohort (n = 76) was then assessed to compare output of the best algorithm against real-life inpatient documentation. RESULTS: For "brain compression", a random forest classifier outperformed other candidate algorithms with an accuracy of 0.81 and area under the curve of 0.90 in the testing dataset. For "brain edema", a random forest classifier again outperformed other candidate algorithms with an accuracy of 0.92 and AUC of 0.94 in the testing dataset. In the provider comparison dataset, for "brain compression," the random forest algorithm demonstrated better accuracy (0.76 vs 0.70) and sensitivity (0.73 vs 0.43) than provider documentation. For "brain edema," the algorithm again demonstrated better accuracy (0.92 vs 0.84) and AUC (0.45 vs 0.09) than provider documentation. DISCUSSION: A natural language processing-based machine learning algorithm can reliably and reproducibly identify selected common neurosurgical comorbidities from radiology reports. CONCLUSION: This result may justify the use of machine learning-based decision support to augment provider documentation.


Asunto(s)
Comorbilidad , Procesamiento de Lenguaje Natural , Humanos , Algoritmos , Pacientes Internos/estadística & datos numéricos , Femenino , Masculino , Aprendizaje Automático , Imagen por Resonancia Magnética/métodos , Documentación , Persona de Mediana Edad , Tomografía Computarizada por Rayos X , Procedimientos Neuroquirúrgicos , Anciano , Aprendizaje Profundo
8.
Sci Rep ; 14(1): 10667, 2024 05 09.
Artículo en Inglés | MEDLINE | ID: mdl-38724576

RESUMEN

The study introduces a new online spike encoding algorithm for spiking neural networks (SNN) and suggests new methods for learning and identifying diagnostic biomarkers using three prominent deep learning neural network models: deep BiLSTM, reservoir SNN, and NeuCube. EEG data from datasets related to epilepsy, migraine, and healthy subjects are employed. Results reveal that BiLSTM hidden neurons capture biological significance, while reservoir SNN activities and NeuCube spiking dynamics identify EEG channels as diagnostic biomarkers. BiLSTM and reservoir SNN achieve 90 and 85% classification accuracy, while NeuCube achieves 97%, all methods pinpointing potential biomarkers like T6, F7, C4, and F8. The research bears implications for refining online EEG classification, analysis, and early brain state diagnosis, enhancing AI models with interpretability and discovery. The proposed techniques hold promise for streamlined brain-computer interfaces and clinical applications, representing a significant advancement in pattern discovery across the three most popular neural network methods for addressing a crucial problem. Further research is planned to study how early can these diagnostic biomarkers predict an onset of brain states.


Asunto(s)
Biomarcadores , Encéfalo , Electroencefalografía , Epilepsia , Trastornos Migrañosos , Redes Neurales de la Computación , Humanos , Electroencefalografía/métodos , Epilepsia/diagnóstico , Epilepsia/fisiopatología , Biomarcadores/análisis , Proyectos Piloto , Trastornos Migrañosos/diagnóstico , Trastornos Migrañosos/fisiopatología , Encéfalo/fisiopatología , Aprendizaje Profundo , Algoritmos , Masculino , Adulto , Femenino
9.
BMC Med Res Methodol ; 24(1): 108, 2024 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-38724903

RESUMEN

OBJECTIVE: Systematic literature reviews (SLRs) are critical for life-science research. However, the manual selection and retrieval of relevant publications can be a time-consuming process. This study aims to (1) develop two disease-specific annotated corpora, one for human papillomavirus (HPV) associated diseases and the other for pneumococcal-associated pediatric diseases (PAPD), and (2) optimize machine- and deep-learning models to facilitate automation of the SLR abstract screening. METHODS: This study constructed two disease-specific SLR screening corpora for HPV and PAPD, which contained citation metadata and corresponding abstracts. Performance was evaluated using precision, recall, accuracy, and F1-score of multiple combinations of machine- and deep-learning algorithms and features such as keywords and MeSH terms. RESULTS AND CONCLUSIONS: The HPV corpus contained 1697 entries, with 538 relevant and 1159 irrelevant articles. The PAPD corpus included 2865 entries, with 711 relevant and 2154 irrelevant articles. Adding additional features beyond title and abstract improved the performance (measured in Accuracy) of machine learning models by 3% for HPV corpus and 2% for PAPD corpus. Transformer-based deep learning models that consistently outperformed conventional machine learning algorithms, highlighting the strength of domain-specific pre-trained language models for SLR abstract screening. This study provides a foundation for the development of more intelligent SLR systems.


Asunto(s)
Aprendizaje Automático , Infecciones por Papillomavirus , Humanos , Infecciones por Papillomavirus/diagnóstico , Economía Médica , Algoritmos , Evaluación de Resultado en la Atención de Salud/métodos , Aprendizaje Profundo , Indización y Redacción de Resúmenes/métodos
10.
BMC Med Imaging ; 24(1): 102, 2024 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-38724896

RESUMEN

Precision and intelligence in evaluating the complexities of middle ear structures are required to diagnose auriculotemporal and ossicle-related diseases within otolaryngology. Due to the complexity of the anatomical details and the varied etiologies of illnesses such as trauma, chronic otitis media, and congenital anomalies, traditional diagnostic procedures may not yield accurate diagnoses. This research intends to enhance the diagnosis of diseases of the auriculotemporal region and ossicles by combining High-Resolution Spiral Computed Tomography (HRSCT) scanning with Deep Learning Techniques (DLT). This study employs a deep learning method, Convolutional Neural Network-UNet (CNN-UNet), to extract sub-pixel information from medical photos. This method equips doctors and researchers with cutting-edge resources, leading to groundbreaking discoveries and better patient healthcare. The research effort is the interaction between the CNN-UNet model and high-resolution Computed Tomography (CT) scans, automating activities including ossicle segmentation, fracture detection, and disruption cause classification, accelerating the diagnostic process and increasing clinical decision-making. The suggested HRSCT-DLT model represents the integration of high-resolution spiral CT scans with the CNN-UNet model, which has been fine-tuned to address the nuances of auriculotemporal and ossicular diseases. This novel combination improves diagnostic efficiency and our overall understanding of these intricate diseases. The results of this study highlight the promise of combining high-resolution CT scanning with the CNN-UNet model in otolaryngology, paving the way for more accurate diagnosis and more individualized treatment plans for patients experiencing auriculotemporal and ossicle-related disruptions.


Asunto(s)
Osículos del Oído , Tomografía Computarizada Espiral , Humanos , Tomografía Computarizada Espiral/métodos , Osículos del Oído/diagnóstico por imagen , Aprendizaje Profundo , Enfermedades del Oído/diagnóstico por imagen , Hueso Temporal/diagnóstico por imagen , Adulto , Redes Neurales de la Computación
11.
BMC Oral Health ; 24(1): 500, 2024 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-38724912

RESUMEN

BACKGROUND: Teeth identification has a pivotal role in the dental curriculum and provides one of the important foundations of clinical practice. Accurately identifying teeth is a vital aspect of dental education and clinical practice, but can be challenging due to the anatomical similarities between categories. In this study, we aim to explore the possibility of using a deep learning model to classify isolated tooth by a set of photographs. METHODS: A collection of 5,100 photographs from 850 isolated human tooth specimens were assembled to serve as the dataset for this study. Each tooth was carefully labeled during the data collection phase through direct observation. We developed a deep learning model that incorporates the state-of-the-art feature extractor and attention mechanism to classify each tooth based on a set of 6 photographs captured from multiple angles. To increase the validity of model evaluation, a voting-based strategy was applied to refine the test set to generate a more reliable label, and the model was evaluated under different types of classification granularities. RESULTS: This deep learning model achieved top-3 accuracies of over 90% in all classification types, with an average AUC of 0.95. The Cohen's Kappa demonstrated good agreement between model prediction and the test set. CONCLUSIONS: This deep learning model can achieve performance comparable to that of human experts and has the potential to become a valuable tool for dental education and various applications in accurately identifying isolated tooth.


Asunto(s)
Aprendizaje Profundo , Diente , Humanos , Diente/anatomía & histología , Diente/diagnóstico por imagen , Fotografía Dental/métodos
12.
BMC Bioinformatics ; 25(1): 182, 2024 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-38724920

RESUMEN

BACKGROUND: The prediction of drug sensitivity plays a crucial role in improving the therapeutic effect of drugs. However, testing the effectiveness of drugs is challenging due to the complex mechanism of drug reactions and the lack of interpretability in most machine learning and deep learning methods. Therefore, it is imperative to establish an interpretable model that receives various cell line and drug feature data to learn drug response mechanisms and achieve stable predictions between available datasets. RESULTS: This study proposes a new and interpretable deep learning model, DrugGene, which integrates gene expression, gene mutation, gene copy number variation of cancer cells, and chemical characteristics of anticancer drugs to predict their sensitivity. This model comprises two different branches of neural networks, where the first involves a hierarchical structure of biological subsystems that uses the biological processes of human cells to form a visual neural network (VNN) and an interpretable deep neural network for human cancer cells. DrugGene receives genotype input from the cell line and detects changes in the subsystem states. We also employ a traditional artificial neural network (ANN) to capture the chemical structural features of drugs. DrugGene generates final drug response predictions by combining VNN and ANN and integrating their outputs into a fully connected layer. The experimental results using drug sensitivity data extracted from the Cancer Drug Sensitivity Genome Database and the Cancer Treatment Response Portal v2 reveal that the proposed model is better than existing prediction methods. Therefore, our model achieves higher accuracy, learns the reaction mechanisms between anticancer drugs and cell lines from various features, and interprets the model's predicted results. CONCLUSIONS: Our method utilizes biological pathways to construct neural networks, which can use genotypes to monitor changes in the state of network subsystems, thereby interpreting the prediction results in the model and achieving satisfactory prediction accuracy. This will help explore new directions in cancer treatment. More available code resources can be downloaded for free from GitHub ( https://github.com/pangweixiong/DrugGene ).


Asunto(s)
Antineoplásicos , Aprendizaje Profundo , Redes Neurales de la Computación , Humanos , Antineoplásicos/farmacología , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Línea Celular Tumoral , Variaciones en el Número de Copia de ADN , Biología Computacional/métodos
13.
BMC Pediatr ; 24(1): 321, 2024 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-38724944

RESUMEN

BACKGROUND: Radiologic volumetric evaluation of Wilms' tumor (WT) is an important indicator to guide treatment decisions. However, due to the heterogeneity of the tumors, radiologists have main-guard differences in diagnosis that can lead to misdiagnosis and poor treatment. The aim of this study was to explore whether CT-based outlining of WT foci can be automated using deep learning. METHODS: We included CT intravenous phase images of 105 patients with WT and double-blind outlining of lesions by two radiologists. Then, we trained an automatic segmentation model using nnUnet. The Dice similarity coefficient (DSC) and 95th percentile Hausdorff distance (HD95) were used to assess the performance. Next, we optimized the automatic segmentation results based on the ratio of the three-dimensional diameter of the lesion to improve the performance of volumetric assessment. RESULTS: The DSC and HD95 was 0.83 ± 0.22 and 10.50 ± 8.98 mm. The absolute difference and percentage difference in tumor size was 72.27 ± 134.84 cm3 and 21.08% ± 30.46%. After optimization according to our method, it decreased to 40.22 ± 96.06 cm3 and 10.16% ± 9.70%. CONCLUSION: We introduce a novel method that enhances the accuracy of predicting WT volume by integrating AI automated outlining and 3D tumor diameters. This approach surpasses the accuracy of using AI outcomes alone and has the potential to enhance the clinical evaluation of pediatric patients with WT. By intertwining AI outcomes with clinical data, this method becomes more interpretive and offers promising applications beyond Wilms tumor, extending to other pediatric diseases.


Asunto(s)
Neoplasias Renales , Tomografía Computarizada por Rayos X , Tumor de Wilms , Humanos , Tumor de Wilms/diagnóstico por imagen , Tumor de Wilms/patología , Neoplasias Renales/diagnóstico por imagen , Neoplasias Renales/patología , Tomografía Computarizada por Rayos X/métodos , Masculino , Femenino , Preescolar , Lactante , Niño , Carga Tumoral , Aprendizaje Profundo , Método Doble Ciego , Imagenología Tridimensional , Estudios Retrospectivos
14.
Brief Bioinform ; 25(3)2024 Mar 27.
Artículo en Inglés | MEDLINE | ID: mdl-38725157

RESUMEN

Cancer, recognized as a primary cause of death worldwide, has profound health implications and incurs a substantial social burden. Numerous efforts have been made to develop cancer treatments, among which anticancer peptides (ACPs) are garnering recognition for their potential applications. While ACP screening is time-consuming and costly, in silico prediction tools provide a way to overcome these challenges. Herein, we present a deep learning model designed to screen ACPs using peptide sequences only. A contrastive learning technique was applied to enhance model performance, yielding better results than a model trained solely on binary classification loss. Furthermore, two independent encoders were employed as a replacement for data augmentation, a technique commonly used in contrastive learning. Our model achieved superior performance on five of six benchmark datasets against previous state-of-the-art models. As prediction tools advance, the potential in peptide-based cancer therapeutics increases, promising a brighter future for oncology research and patient care.


Asunto(s)
Antineoplásicos , Aprendizaje Profundo , Péptidos , Péptidos/química , Péptidos/uso terapéutico , Humanos , Antineoplásicos/uso terapéutico , Antineoplásicos/química , Neoplasias/tratamiento farmacológico , Biología Computacional/métodos , Aprendizaje Automático , Algoritmos
15.
Cells ; 13(9)2024 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-38727307

RESUMEN

Tumor necrosis factor-α-induced protein 8-like 3 (TNFAIP8L3 or TIPE3) functions as a transfer protein for lipid second messengers. TIPE3 is highly upregulated in several human cancers and has been established to significantly promote tumor cell proliferation, migration, and invasion and inhibit the apoptosis of cancer cells. Thus, inhibiting the function of TIPE3 is expected to be an effective strategy against cancer. The advancement of artificial intelligence (AI)-driven drug development has recently invigorated research in anti-cancer drug development. In this work, we incorporated DFCNN, Autodock Vina docking, DeepBindBC, MD, and metadynamics to efficiently identify inhibitors of TIPE3 from a ZINC compound dataset. Six potential candidates were selected for further experimental study to validate their anti-tumor activity. Among these, three small-molecule compounds (K784-8160, E745-0011, and 7238-1516) showed significant anti-tumor activity in vitro, leading to reduced tumor cell viability, proliferation, and migration and enhanced apoptotic tumor cell death. Notably, E745-0011 and 7238-1516 exhibited selective cytotoxicity toward tumor cells with high TIPE3 expression while having little or no effect on normal human cells or tumor cells with low TIPE3 expression. A molecular docking analysis further supported their interactions with TIPE3, highlighting hydrophobic interactions and their shared interaction residues and offering insights for designing more effective inhibitors. Taken together, this work demonstrates the feasibility of incorporating deep learning and MD simulations in virtual drug screening and provides inhibitors with significant potential for anti-cancer drug development against TIPE3-.


Asunto(s)
Proliferación Celular , Aprendizaje Profundo , Péptidos y Proteínas de Señalización Intracelular , Simulación del Acoplamiento Molecular , Humanos , Proliferación Celular/efectos de los fármacos , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Péptidos y Proteínas de Señalización Intracelular/antagonistas & inhibidores , Línea Celular Tumoral , Movimiento Celular/efectos de los fármacos , Antineoplásicos/farmacología , Apoptosis/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/farmacología , Bibliotecas de Moléculas Pequeñas/química , Neoplasias/tratamiento farmacológico , Neoplasias/metabolismo , Neoplasias/patología
16.
PLoS One ; 19(5): e0299696, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38728335

RESUMEN

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 disease, which represents a new life-threatening disaster. Regarding viral infection, many therapeutics have been investigated to alleviate the epidemiology such as vaccines and receptor decoys. However, the continuous mutating coronavirus, especially the variants of Delta and Omicron, are tended to invalidate the therapeutic biological product. Thus, it is necessary to develop molecular entities as broad-spectrum antiviral drugs. Coronavirus replication is controlled by the viral 3-chymotrypsin-like cysteine protease (3CLpro) enzyme, which is required for the virus's life cycle. In the cases of severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV), 3CLpro has been shown to be a promising therapeutic development target. Here we proposed an attention-based deep learning framework for molecular graphs and sequences, training from the BindingDB 3CLpro dataset (114,555 compounds). After construction of such model, we conducted large-scale screening the in vivo/vitro dataset (276,003 compounds) from Zinc Database and visualize the candidate compounds with attention score. geometric-based affinity prediction was employed for validation. Finally, we established a 3CLpro-specific deep learning framework, namely GraphDPI-3CL (AUROC: 0.958) achieved superior performance beyond the existing state of the art model and discovered 10 molecules with a high binding affinity of 3CLpro and superior binding mode.


Asunto(s)
Antivirales , Tratamiento Farmacológico de COVID-19 , Aprendizaje Profundo , SARS-CoV-2 , SARS-CoV-2/efectos de los fármacos , SARS-CoV-2/metabolismo , SARS-CoV-2/genética , Antivirales/farmacología , Antivirales/uso terapéutico , Humanos , Proteasas 3C de Coronavirus/metabolismo , Proteasas 3C de Coronavirus/antagonistas & inhibidores , Unión Proteica , COVID-19/virología , Simulación del Acoplamiento Molecular
17.
Sci Adv ; 10(19): eadj6990, 2024 May 10.
Artículo en Inglés | MEDLINE | ID: mdl-38728404

RESUMEN

Mosquito-borne diseases like malaria are rising globally, and improved mosquito vector surveillance is needed. Survival of Anopheles mosquitoes is key for epidemiological monitoring of malaria transmission and evaluation of vector control strategies targeting mosquito longevity, as the risk of pathogen transmission increases with mosquito age. However, the available tools to estimate field mosquito age are often approximate and time-consuming. Here, we show a rapid method that combines matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry with deep learning for mosquito age prediction. Using 2763 mass spectra from the head, legs, and thorax of 251 field-collected Anopheles arabiensis mosquitoes, we developed deep learning models that achieved a best mean absolute error of 1.74 days. We also demonstrate consistent performance at two ecological sites in Senegal, supported by age-related protein changes. Our approach is promising for malaria control and the field of vector biology, benefiting other disease vectors like Aedes mosquitoes.


Asunto(s)
Anopheles , Aprendizaje Profundo , Mosquitos Vectores , Animales , Anopheles/fisiología , Mosquitos Vectores/fisiología , Malaria/transmisión , Malaria/prevención & control , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/métodos , Senegal , Espectrometría de Masas/métodos , Envejecimiento/fisiología
18.
J Pak Med Assoc ; 74(4 (Supple-4)): S43-S48, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38712408

RESUMEN

This narrative review explores the transformative potential of Artificial Intelligence (AI) and advanced imaging techniques in predicting Pathological Complete Response (pCR) in Breast Cancer (BC) patients undergoing Neo-Adjuvant Chemotherapy (NACT). Summarizing recent research findings underscores the significant strides made in the accurate assessment of pCR using AI, including deep learning and radiomics. Such AI-driven models offer promise in optimizing clinical decisions, personalizing treatment strategies, and potentially reducing the burden of unnecessary treatments, thereby improving patient outcomes. Furthermore, the review acknowledges the potential of AI to address healthcare disparities in Low- and Middle-Income Countries (LMICs), where accessible and scalable AI solutions may enhance BC management. Collaboration and international efforts are essential to fully unlock the potential of AI in BC care, offering hope for a more equitable and effective approach to treatment worldwide.


Asunto(s)
Inteligencia Artificial , Neoplasias de la Mama , Humanos , Neoplasias de la Mama/terapia , Neoplasias de la Mama/diagnóstico por imagen , Neoplasias de la Mama/patología , Femenino , Terapia Neoadyuvante/métodos , Aprendizaje Profundo , Quimioterapia Adyuvante
19.
Sci Rep ; 14(1): 10664, 2024 05 09.
Artículo en Inglés | MEDLINE | ID: mdl-38724603

RESUMEN

Kiwifruit soft rot is highly contagious and causes serious economic loss. Therefore, early detection and elimination of soft rot are important for postharvest treatment and storage of kiwifruit. This study aims to accurately detect kiwifruit soft rot based on hyperspectral images by using a deep learning approach for image classification. A dual-branch selective attention capsule network (DBSACaps) was proposed to improve the classification accuracy. The network uses two branches to separately extract the spectral and spatial features so as to reduce their mutual interference, followed by fusion of the two features through the attention mechanism. Capsule network was used instead of convolutional neural networks to extract the features and complete the classification. Compared with existing methods, the proposed method exhibited the best classification performance on the kiwifruit soft rot dataset, with an overall accuracy of 97.08% and a 97.83% accuracy for soft rot. Our results confirm that potential soft rot of kiwifruit can be detected using hyperspectral images, which may contribute to the construction of smart agriculture.


Asunto(s)
Actinidia , Redes Neurales de la Computación , Enfermedades de las Plantas , Actinidia/microbiología , Enfermedades de las Plantas/microbiología , Aprendizaje Profundo , Imágenes Hiperespectrales/métodos , Frutas/microbiología , Procesamiento de Imagen Asistido por Computador/métodos
20.
Sci Rep ; 14(1): 10753, 2024 05 10.
Artículo en Inglés | MEDLINE | ID: mdl-38730248

RESUMEN

This paper proposes an approach to enhance the differentiation task between benign and malignant Breast Tumors (BT) using histopathology images from the BreakHis dataset. The main stages involve preprocessing, which encompasses image resizing, data partitioning (training and testing sets), followed by data augmentation techniques. Both feature extraction and classification tasks are employed by a Custom CNN. The experimental results show that the proposed approach using the Custom CNN model exhibits better performance with an accuracy of 84% than applying the same approach using other pretrained models, including MobileNetV3, EfficientNetB0, Vgg16, and ResNet50V2, that present relatively lower accuracies, ranging from 74 to 82%; these four models are used as both feature extractors and classifiers. To increase the accuracy and other performance metrics, Grey Wolf Optimization (GWO), and Modified Gorilla Troops Optimization (MGTO) metaheuristic optimizers are applied to each model separately for hyperparameter tuning. In this case, the experimental results show that the Custom CNN model, refined with MGTO optimization, reaches an exceptional accuracy of 93.13% in just 10 iterations, outperforming the other state-of-the-art methods, and the other four used pretrained models based on the BreakHis dataset.


Asunto(s)
Neoplasias de la Mama , Aprendizaje Profundo , Humanos , Neoplasias de la Mama/clasificación , Neoplasias de la Mama/patología , Neoplasias de la Mama/diagnóstico , Femenino , Redes Neurales de la Computación , Procesamiento de Imagen Asistido por Computador/métodos , Algoritmos
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