Test Set Validation Research Articles

NO classifier prediction of anti neuroinflammatory agents using text mining of 3D molecular fingerprints.

CNS Drug discovery has been challenging due to the lack of clarity on CNS diseases' basic biological and pathological mechanisms. Despite the difficulty, some CNS drugs have been developed based on phenotypic effects. Herein, we propose a phenotype-structure relationship model, which predicts an anti-neuroinflammatory potency based on 3D molecular structures of the phenotype-active or inactive compounds without specifying targets. For this chemo-centric study, a predictive model of the nitric oxide (NO) inhibitory potency in hyper-activated microglia is built from the 548 agents, which were collected from 95 research articles (28 substructures consisting of natural products and synthetic scaffolds) and doubly externally validated by the agents of 9 research articles as third set. 3D Structures (multi-conformer ensemble) of every agent were encoded into the E3FP molecular fingerprint of the Keiser group as a 3D molecular representation. The location information of the molecular fingerprints could be learned and validated to classify the inhibitory potency of compounds (IC50 cut-off between the active and inactive: 37.1 µM): (1) multi-layer perceptron (MLP) (AUC-CV: 0.997, AUC-Test: 0.992), (2) recurrent neural network (RNN) (AUC-CV: 0.999, AUC-Test: 0.995), and (3) convolutional neural network (CNN) (AUC-CV: 0.998, AUC-Test: 0.994). The high performance of these models was compared with that of four classical machine classification models (Logistic, Ridge, Lasso, and Naïve Bayes). We named the binary classification models NO-Classifier. Independent test set validation and decision region analysis of the independent test set doubly demonstrated NO-Classifier effectively discerned the anti-inflammatory potency of testing compounds in inflammatory cell phenotype with the webserver in https://no-classifier.onrender.com.

T4Seeker: a hybrid model for type IV secretion effectors identification.

The type IV secretion system is widely present in various bacteria, such as Salmonella, Escherichia coli, and Helicobacter pylori. These bacteria use the type IV secretion system to secrete type IV secretion effectors, infect host cells, and disrupt or modulate the communication pathways. In this study, type III and type VI secretion effectors were used as negative samples to train a robust model. The area under the curve of T4Seeker on the validation and independent test sets were 0.947 and 0.970, respectively, demonstrating the strong predictive capacity and robustness of T4Seeker. After comparing with the classic and state-of-the-art T4SE identification models, we found that T4Seeker, which is based on traditional features and large language model features, had a higher predictive ability. The T4Seeker proposed in this study demonstrates superior performance in the field of T4SEs prediction. By integrating features at multiple levels, it achieves higher predictive accuracy and strong generalization capability, providing an effective tool for future T4SE research.

Artificial Intelligence (AI)-Driven Frailty Prediction Using Electronic Health Records in Hospitalized Patients With Cardiovascular Disease.

This study aimed to create a deep learning model for predicting phenotypic physical frailty from electronic medical record information in patients with cardiovascular disease. This single-center retrospective study enrolled patients who could be assessed for physical frailty according to cardiovascular health study criteria (25.5% [691/2,705] of the patients were frail). Patients were randomly separated for training (Train set: 80%) and validation (Test set: 20%) of the deep learning model. Multiple models were created using LightGBM, random forest, and logistic regression for deep learning, and their predictive abilities were compared. The LightGBM model had the highest accuracy (in a Test set: F1 score 0.561; accuracy 0.726; area under the curve of the receiver operating characteristics [AUC] 0.804). These results using only commonly used blood biochemistry test indices (in a Test set: F1 score 0.551; accuracy 0.721; AUC 0.793) were similar. The created models were consistently and strongly associated with physical functions at hospital discharge, all-cause death, and heart failure-related readmission. Deep learning models derived from large sample sizes of phenotypic physical frailty have shown good accuracy and consistent associations with prognosis and physical functions.

A Novel Machine Learning-Based Predictive Model of Clinically Significant Prostate Cancer and Online Risk Calculator

ObjectivesTo create a machine learning predictive model combining PI-RADS score, PSA density, and clinical variables to predict clinically significant prostate cancer (csPCa). MethodsWe evaluated a cohort of patients who underwent prostate biopsy for suspected prostate cancer (PCa) in New Zealand, Australia, and Switzerland. We collected data on age, body mass index (BMI), PSA level, prostate volume, PSA density (PSAD), PI-RADS scores, previous biopsy, and corresponding histology results. The dataset was divided into derivation (training) and validation (test) sets using random splits. An independent dataset was obtained from the Harvard Dataverse for external validation. A cohort of 1272 patients was analyzed. We fitted a Lasso model, XGBoost, and LightGBM to the training set and assessed their accuracy. ResultsAll models demonstrated ROC AUC values ranging from 0.830 to 0.851. LightGBM was considered the superior model, with an ROC of 0.851 [95%CI: 0.804 – 0.897] in the test set and 0.818 [95% CI: 0.798 – 0.831] in the external dataset. The most important variable was PI-RADS, followed by PSA density, history of previous biopsy, age, and BMI. ConclusionsWe developed a predictive model for detecting csPCa that exhibited a high ROC-AUC value for internal and external validations. This suggests that the integration of the clinical parameters outperformed each individual predictor. Additionally, the model demonstrated good calibration metrics, indicative of a more balanced model than the existing models.

IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation.

As an emerging class of RNA molecules, circular RNAs play pivotal roles in various biological processes, thereby determining their three-dimensional (3D) structure is crucial for a deep understanding of their biological significances. Similar to linear RNAs, the development of computational methods for circular RNA 3D structure prediction is challenging, especially considering the inherent flexibility and potentially long length of circular RNAs. Here, we introduce an extension of our previous IsRNA2 model, named IsRNAcirc, to enable circular RNA 3D structure predictions through coarse-grained molecular dynamics simulations. The workflow of IsRNAcirc consists of four main steps, including input preparation, end closure, structure prediction, and model refinement. Our results demonstrate that IsRNAcirc can provide reasonable 3D structure predictions for circular RNAs, which significantly reduce the locally irrational elements contained in the initial input. Moreover, for a validation test set comprising 34 circular RNAs, our IsRNAcirc can generate 3D models with better scores than the template-based 3dRNA method. These findings demonstrate that our IsRNAcirc method is a promising tool to explore the structural details along with intricate interactions of circular RNAs.

Construction and validation of a line chart for gestational diabetes mellitus based on clinical indicators

BackgroundGestational diabetes mellitus (GDM) is a common complication of mid–to-late pregnancy. Here, we constructed a predictive model for GDM based on a combination of clinical characteristics and relevant serum markers.MethodsData from full-term singleton vaginal deliveries from January 2022 to January 2023 were retrospectively collected from the obstetrics department. The data collected were segregated and assigned to training, validation, and external test sets. Maternal demographic characteristics, living and working habits, and haematological indicators, such as liver function and lipids were collected using a questionnaire designed for the study. The “rms” package in R was used to explore GDM-associated factors through stepwise regression at P < 0.05. A predictive model was developed based on the results of multifactorial logistic regression analysis. We then evaluated the differentiation of the column-line graphical model and performed internal and external validation. To assess the accuracy of the bar graphical model, we plotted calibration and decision curves.ResultsData from 265 pregnant women were included in the training and internal validation sets, and data from 113 pregnant women were included in the external validation set. The logistic regression algorithm screened 8 indicators as predictors. A prediction model was constructed with ALT, TBA, TC, and TG levels while considering whether GDM affects appetite, the husband– wife relationship, family history, and parental relationships as predictors. The Hosmer–Lemeshow goodness-of-fit test revealed that the chi-square values for the modelling, internal validation, and external validation groups (χ2 = 5.964, 3.249, and 12.182, respectively) were all P > 0.05. The ROC curve AUCs for the three groups were 0.93 (95% CI: 0.89–0.97), 0.72 (95% CI: 0.62–0.81), and 0.68 (95% CI: 0.53–0.83), respectively.ConclusionIn this study, a GDM prediction model was constructed to achieve high performance in GDM risk prediction based on routine obstetric tests and information.

Early prediction of sepsis in emergency department patients using various methods and scoring systems.

Early recognition of sepsis, a common life-threatening condition in intensive care units (ICUs), is beneficial for improving patient outcomes. However, most sepsis prediction models were trained and assessed in the ICU, which might not apply to emergency department (ED) settings. To establish an early predictive model based on basic but essential information collected upon ED presentation for the follow-up diagnosis of sepsis observed in the ICU. This study developed and validated a reliable model of sepsis prediction among ED patients by comparing 10 different methods based on retrospective electronic health record data from the MIMIC-IV database. In-ICU sepsis was identified as the primary outcome. The potential predictors encompassed baseline demographics, vital signs, pain scale, chief complaints and Emergency Severity Index (ESI). 80% and 20% of the total of 425 737 ED visit records were randomly selected for the train set and the test set for model development and validation, respectively. Among the methods evaluated, XGBoost demonstrated an optimal predictive performance with an area under the curve (AUC) of 0.90 (95% CI: 0.90-0.91). Logistic regression exhibited a comparable predictive ability to XGBoost, with an AUC of 0.89 (95% CI: 0.89-0.90), along with a sensitivity and specificity of 85% (95% CI: 0.83-0.86) and 78% (95% CI: 0.77-0.80), respectively. Neither of the five commonly used severity scoring systems demonstrated satisfactory performance for sepsis prediction. The predictive ability of using ESI as the sole predictor (AUC: 0.79, 95% CI: 0.78-0.80) was also inferior to the model integrating ESI and other basic information. The use of ESI combined with basic clinical information upon ED presentation accurately predicted sepsis among ED patients, strengthening its application in ED. The proposed model may assist nurses in risk stratification management and prioritize interventions for potential sepsis patients, even in low-resource settings.

Integrating VAI-Assisted Quantified CXRs and Multimodal Data to Assess the Risk of Mortality.

To address the unmet need for a widely available examination for mortality prediction, this study developed a foundation visual artificial intelligence (VAI) to enhance mortality risk stratification using chest X-rays (CXRs). The VAI employed deep learning to extract CXR features and a Cox proportional hazard model to generate a hazard score ("CXR-risk"). We retrospectively collected CXRs from patients visited outpatient department and physical examination center. Subsequently, we reviewed mortality and morbidity outcomes from electronic medical records. The dataset consisted of 41,945, 10,492, 31,707, and 4441 patients in the training, validation, internal test, and external test sets, respectively. During the median follow-up of 3.2 (IQR, 1.2-6.1) years of both internal and external test sets, the "CXR-risk" demonstrated C-indexes of 0.859 (95% confidence interval (CI), 0.851-0.867) and 0.870 (95% CI, 0.844-0.896), respectively. Patients with high "CXR-risk," above 85th percentile, had a significantly higher risk of mortality than those with low risk, below 50th percentile. The addition of clinical and laboratory data and radiographic report further improved the predictive accuracy, resulting in C-indexes of 0.888 and 0.900. The VAI can provide accurate predictions of mortality and morbidity outcomes using just a single CXR, and it can complement other risk prediction indicators to assist physicians in assessing patient risk more effectively.

Artificial intelligence applied to development of predictive stability model for intracranial aneurysms

BackgroundWe aimed to develop multiple machine learning models to predict the risk of early intracranial aneurysms (IAs) rupture, evaluate and compare the performance of predictive models.MethodsInformation related to patients diagnosed with IA by CT angiography and clinicians in Central hospital of Dalian University of Technology from January 2010 to June 2022 was collected, including clinical characteristics, blood indicators and IA morphological parameters. IA with rupture or maximum growth ≥ 0.5 mm within 1 month of first diagnosis was considered unstable. The relevant factors affecting IA stability were screened and predictive models were developed based on the above three levels, including random forest (RF), support vector machine (SVM), and artificial neural network (ANN). Sensitivity, specificity, accuracy and area under curve (AUC) value were used to evaluate the predictive models.ResultsA total of 989 IA patients were included in the study, including 561 stable patients and 428 unstable patients. For RF models, the training set showed that sensitivity, specificity, accuracy and the AUC values were 72.8–83.7%, 76.9–86.9%, 75.1–84.1% and 0.748 (0.719–0.778)–0.839 (0.814–0.864), respectively; after test set validation, the results were 71.9–78.8%, 75.0–84.0%, 73.6–81.1% and 0.734 (0.688–0.781)–0.809 (0.768–0.850), respectively. For SVM models, the training set were 66.0–80.2%, 76.5–85.5%, 71.7–82.3%, 0.712 (0.682–0.743)–0.913 (0.884–0.924), respectively; the test set were 44.2–78.3%, 63.4–84.4%, 57.9–80.9%, 0.699 (0.651–0.747)–0.806 (0.765–0.848), respectively. For ANN models, the training set were 66.8–83.0%, 75.3–82.3%, 71.6–82.1%, 0.783 (0.757–0.808)–0.897 (0.879–0.914); the test set were 63.1–76.3%, 65.5–84.0%, 64.4–80.6%, 0.680 (0.593–0.694)–0.860 (0.821–0.899). The results of variable importance showed that age, white blood cell count (WBC) and uric acid (UA) played an important role in predicting the stability of IA.ConclusionsThe predictive stability models of IA based on three artificial intelligence methods shows good clinical application. Age, WBC and UA played an important role in predicting the IA stability, and were potentially important predictors.

Microwave cavity antenna for automatic detection of chicken breast muscles affected by wooden breast defect

Over the past years, artificial selection for meat-type (broiler) chickens has resulted in improved production efficiency, but also in an increased incidence of skeletal muscle abnormalities. In particular, wooden breast (WB) abnormality causes abrupt changes in meat quality and enormous economic losses. Thus, the poultry processing industry requires a reliable method to detect the abnormality in production lines in a non-destructive and contactless way. The present research aimed to evaluate the effect of WB on dielectric properties to develop a potential online technique to distinguish unaffected from affected breasts. Sixty-five pectoralis major muscles were picked 3 h post-mortem from the same flock (42-day-old broilers, 2.8 kg average live weight) and classified by visual inspection according to their phenotype as normal (N, not showing not any signs of the WB condition; n = 33) or WB (exhibiting extensive hardened areas and stiffness perceived by manual palpation throughout the entire fillet; n = 32). WB muscles exhibited remarkably higher values of dielectric constant and loss factor in a wide range of the explored frequencies (200 MHz–14 GHz), suggesting higher water mobility and a higher solvate capacity; this makes the electromagnetic technique for classification promising. Based on the above evidence, a rapid microwave electric technique in the range 1.5 GHz–3 GHz was developed for the online detection of WB. Indeed, combining the use of a cavity antenna (vector network analyzer instrumental chain with partial least square – discriminant analysis), this technique correctly classified 100% of the validation test set.

Video-based AI module with raw-scale and ROI-scale information for thyroid nodule diagnosis

ObjectivesUltrasound examination is a primary method for detecting thyroid lesions in clinical practice. Incorrect ultrasound diagnosis may lead to delayed treatment or unnecessary biopsy punctures. Therefore, our objective is to propose an artificial intelligence model to increase the precision of thyroid ultrasound diagnosis and reduce puncture rates. MethodsWe consecutively collected ultrasound recordings from 672 patients with 845 nodules across two Chinese hospitals. This dataset was divided into training, validation, and internal test sets in a ratio of 7:1:2. We constructed and tested six different model variants based on different video feature distillation strategies and whether additional information from ROI (Region of Interest) scales was used. The models' performances were evaluated using the internal test set and an additional external test set containing 126 nodules from a third hospital. ResultsThe dual-stream model, which contains both raw-scale and ROI-scale streams with the time dimensional convolution layer, achieved the best performance on both internal and external test sets. On the internal test set, it achieved an AUROC (Area Under Receiver Operating Characteristic Curve) of 0.969 (95 % confidence interval, CI: 0.944–0.993) and an accuracy of 92.6 %, outperforming other variants (AUROC: 0.936–0.955, accuracy: 80.2%–88.3 %) and experienced radiologists (accuracy: 91.9 %). The AUROC of the best model in the external test was 0.931 (95 % CI: 0.890–0.972). ConclusionIntegrating a dual-stream model with additional ROI scale information and the time dimensional convolution layer can improve performance in diagnosing thyroid ultrasound videos.

Enhancing Manufacturing Processing Stability and Efficiency with Linear-Regression Analysis: Modeling on a Flow-Drill Screw (FDS) Joining Process

The instability (in processing time) in the flow-drill screwing process is undesired but inescapable due to variations in material property, gauge, and process parameters. A substantial number of materials and lab labor need to be used to test and control the variability of the real manufacturing joining process. To enhance the stability and efficiency of the screwing process, this study seeks multi-disciplinary collaboration by applying linear-regression modeling. Six hundred and forty-eight data points were collected and split into an 80% training set for model building and a 20% test set for model validation. A multiple linear-regression model was built. The results indicated that, compared to variable base level (6000 rpm rotational speed and 1100 N downforce), higher rotational speed (8000 rpm, 7000 rpm), greater downforce (1200 N, 1300 N), and their interaction were significantly associated with passage (processing) time, while the switch point did not significantly affect passage time. The interaction plot and effect size were adopted to provide measurements of the effect magnitude on processing time. The coefficient of determination indicated that 86% of the variability in the passage time can be explained by this model. Statistical analysis, such as data visualization, statistical modeling, and other data-driven analysis methods, can be used to detect underlying relationships between variables, investigate variations, and make predictions in the manufacturing process. The outcomes from the data-driven analysis can benefit from improving the economical manufacturing system, refining the processing setting, and reducing test material costs, labor, and lead time.

MRDPDA: A multi-Laplacian regularized deepFM model for predicting piRNA-disease associations.

PIWI-interacting RNAs (piRNAs) are a typical class of small non-coding RNAs, which are essential for gene regulation, genome stability and so on. Accumulating studies have revealed that piRNAs have significant potential as biomarkers and therapeutic targets for a variety of diseases. However current computational methods face the challenge in effectively capturing piRNA-disease associations (PDAs) from limited data. In this study, we propose a novel method, MRDPDA, for predicting PDAs based on limited data from multiple sources. Specifically, MRDPDA integrates a deep factorization machine (deepFM) model with regularizations derived from multiple yet limited datasets, utilizing separate Laplacians instead of a simple average similarity network. Moreover, a unified objective function to combine embedding loss about similarities is proposed to ensure that the embedding is suitable for the prediction task. In addition, a balanced benchmark dataset based on piRPheno is constructed and a deep autoencoder is applied for creating reliable negative set from the unlabeled dataset. Compared with three latest methods, MRDPDA achieves the best performance on the pirpheno dataset in terms of the five-fold cross validation test and independent test set, and case studies further demonstrate the effectiveness of MRDPDA.

Identification of novel PHGDH inhibitors based on computational investigation: an all-in-one combination strategy to develop potential anti-cancer candidates.

Biological studies have elucidated that phosphoglycerate dehydrogenase (PHGDH) is the rate-limiting enzyme in the serine synthesis pathway in humans that is abnormally expressed in numerous cancers. Inhibition of the PHGDH activity is thought to be an attractive approach for novel anti-cancer therapy. The development of structurally diverse novel PHGDH inhibitors with high efficiency and low toxicity is a promising drug discovery strategy. A ligand-based 3D-QSAR pharmacophore model was developed using the HypoGen algorithm methodology of Discovery Studio. The selected pharmacophore model was further validated by test set validation, cost analysis, and Fischer randomization validation and was then used as a 3D query to screen compound libraries with various chemical scaffolds. The estimated activity, drug-likeness, molecular docking, growing scaffold, and molecular dynamics simulation processes were applied in combination to reduce the number of virtual hits. The potential candidates against PHGDH were screened based on estimated activity, docking scores, predictive absorption, distribution, metabolism, excretion, and toxicity (ADME/T) properties, and molecular dynamics simulation. Finally, an all-in-one combination was employed successfully to design and develop three potential anti-cancer candidates.

Lesion Localization and Pathological Diagnosis of Ovine Pulmonary Adenocarcinoma Based on MASK R-CNN.

Ovine pulmonary adenocarcinoma (OPA) is a contagious lung tumour caused by the Jaagsiekte Sheep Retrovirus (JSRV). Histopathological diagnosis is the gold standard for OPA diagnosis. However, interpretation of traditional pathology images is complex and operator dependent. The mask regional convolutional neural network (Mask R-CNN) has emerged as a valuable tool in pathological diagnosis. This study utilized 54 typical OPA whole slide images (WSI) to extract 7167 typical lesion images containing OPA to construct a Common Objects in Context (COCO) dataset for OPA pathological images. The dataset was categorized into training and test sets (8:2 ratio) for model training and validation. Mean average specificity (mASp) and average sensitivity (ASe) were used to evaluate model performance. Six WSI-level pathological images (three OPA and three non-OPA images), not included in the dataset, were used for anti-peeking model validation. A random selection of 500 images, not included in the dataset establishment, was used to compare the performance of the model with assessment by pathologists. Accuracy, sensitivity, specificity, and concordance rate were evaluated. The model achieved a mASp of 0.573 and an ASe of 0.745, demonstrating effective lesion detection and alignment with expert annotation. In Anti-Peeking verification, the model showed good performance in locating OPA lesions and distinguished OPA from non-OPA pathological images. In the random 500-image diagnosis, the model achieved 92.8% accuracy, 100% sensitivity, and 88% specificity. The agreement rates between junior and senior pathologists were 100% and 96.5%, respectively. In conclusion, the Mask R-CNN-based OPA diagnostic model developed for OPA facilitates rapid and accurate diagnosis in practical applications.

Flow Injection Analysis With UV Detection Versus Raman Spectroscopy for the Quantitative Analysis of Remdesivir

ABSTRACTThe quality and the security of preparations in hospital centres are essential to guarantee the patient's safety. The development of fast and efficient analytical methods is required to control the finished product before use. In this context, the study aimed to compare the performance and interchangeability of two spectral analytical methods: the flow injection analysis (FIA) with UV detection and the Raman spectroscopy for the quality control of preparation before use to quantify the remdesivir as a SARS‐CoV‐2 drug. A quantitative study of remdesivir was performed using clinically relevant concentration solutions ranging from 0.25 to 1.625 mg.mL−1 in 0.9% NaCl. Samples were analysed by FIA‐UV at 245 nm and by a handheld Raman spectroscopy at 785 nm. Quantitative models were developed using a calibration set (n = 45 samples) and optimized using a validation set (n = 27). An external validation test set (n = 58) was used to compare the two methods by a Bland–Altman plot. Partial least square regression was used to analyse Raman spectra, while univariate analysis was performed at 245 nm for FIA‐UV. The regression coefficient was higher than 0.990 for both methods, and the root mean square error of prediction was 0.031 mg.mL−1 for Raman spectroscopy. The Bland–Altman plot confirmed the interchangeability of the two methods and the potential of Raman spectroscopy to control remdesivir during clinical preparation in the hospital.

Prediction of neurologic outcome after out-of-hospital cardiac arrest: An interpretable approach with machine learning

Out-of-hospital cardiac arrest (OHCA) is a critical condition with low survival rates. In patients with a return of spontaneous circulation, brain injury is a leading cause of death.In this study, we propose an interpretable machine learning approach for predicting neurologic outcome after OHCA, using information available at the time of hospital admission. MethodsThe study population were 55 615 OHCA cases registered in the Swedish Cardiopulmonary Resuscitation Registry between 2010 and 2020. The dataset was split to training and validation sets (for model development) and test set (for evaluation of the final model). We used an XGBoost algorithm with stratified, repeated 10-fold cross-validation along with Optuna framework for hyperparameters tuning. The final model was trained on 10 features selected based on the importance scores and evaluated on the test set in terms of discrimination, calibration and bias-variance tradeoff. We used SHapley Additive exPlanations to address the ‘black-box’ model and align with eXplainable artificial intelligence. ResultsThe final model achieved: area under the receiver operating characteristic value 0.964 (95% confidence interval (CI) [0.960–0.968]), sensitivity 0.606 (95% CI [0.573–0.634]), specificity 0.975 (95% CI [0.972–0.978]), positive predictive value (PPV) 0.664 (95% CI [0.625–0.696]), negative predictive value (NPV) 0.969 (95% CI [0.966–0.972]), macro F1 0.803 (95% CI [0.788–0.816]), and showed a very good calibration. SHAP features with the highest impact on the model’s output were:’ROSC on arrival to hospital’, ‘Initial rhythm asystole’ and ‘Conscious on arrival to hospital’. ConclusionsThe XGBoost machine learning model with 10 features available at the time of hospital admission showed good performance for predicting neurologic outcome after OHCA, with no apparent signs of overfitting.

Deep learning-based detection of primary bone tumors around the knee joint on radiographs: a multicenter study.

Most primary bone tumors are often found in the bone around the knee joint. However, the detection of primary bone tumors on radiographs can be challenging for the inexperienced or junior radiologist. This study aimed to develop a deep learning (DL) model for the detection of primary bone tumors around the knee joint on radiographs. From four tertiary referral centers, we recruited 687 patients diagnosed with bone tumors (including osteosarcoma, chondrosarcoma, giant cell tumor of bone, bone cyst, enchondroma, fibrous dysplasia, etc.; 417 males, 270 females; mean age 22.8±13.2 years) by postoperative pathology or clinical imaging/follow-up, and 1,988 participants with normal bone radiographs (1,152 males, 836 females; mean age 27.9±12.2 years). The dataset was split into a training set for model development, an internal independent and an external test set for model validation. The trained model located bone tumor lesions and then detected tumor patients. Receiver operating characteristic curves and Cohen's kappa coefficient were used for evaluating detection performance. We compared the model's detection performance with that of two junior radiologists in the internal test set using permutation tests. The DL model correctly localized 94.5% and 92.9% bone tumors on radiographs in the internal and external test set, respectively. An accuracy of 0.964/0.920, and an area under the receiver operating characteristic curve (AUC) of 0.981/0.990 in DL detection of bone tumor patients were for the internal and external test set, respectively. Cohen's kappa coefficient of the model in the internal test set was significantly higher than that of the two junior radiologists with 4 and 3 years of experience in musculoskeletal radiology (Model vs. Reader A, 0.927 vs. 0.777, P<0.001; Model vs. Reader B, 0.927 vs. 0.841, P=0.033). The DL model achieved good performance in detecting primary bone tumors around the knee joint. This model had better performance than those of junior radiologists, indicating the potential for the detection of bone tumors on radiographs.

Raman spectroscopy as a tool for characterisation of quality parameters in Norwegian grown apples during ripening

This study shows for the first time the feasibility of Raman spectroscopy as a non-destructive method to follow the ripening process of apple fruits. Two different varieties of apples were studied: ‘Aroma’ and ‘Elstar’. By visual inspection, Raman spectra showed that the starch content was higher in ‘Elstar’ apples compared to ‘Aroma’. The degradation of starch over time could be detected in the Raman spectra, indicating that the method can be used to monitor the ripening process. The ripeness markers starch index, soluble solids content (SSC), and the sugars glucose, fructose and sucrose were determined with traditional destructive methods. Cross validated calibration models based on Raman spectroscopy were obtained for all quality parameters, and test set validation offered good results, with R2 in the range 0.4–0.86 for ‘Aroma’ and 0.4–0.95 for ‘Elstar’, respectively. The regression coefficients showed that the calibrations relied on Raman bands associated with starch and different sugars. The results suggest that Raman spectroscopy in the future could be used to determine the optimal time of harvesting and to sort apples into different degrees of ripeness.

Habitat radiomics and deep learning fusion nomogram to predict EGFR mutation status in stage I non-small cell lung cancer: a multicenter study

Develop a radiomics nomogram that integrates deep learning, radiomics, and clinical variables to predict epidermal growth factor receptor (EGFR) mutation status in patients with stage I non-small cell lung cancer (NSCLC). We retrospectively included 438 patients who underwent curative surgery and completed driver-gene mutation tests for stage I NSCLC from four academic medical centers. Predictive models were established by extracting and analyzing radiomic features in intratumoral, peritumoral, and habitat regions of CT images to identify EGFR mutation status in stage I NSCLC. Additionally, three deep learning models based on the intratumoral region were constructed. A nomogram was developed by integrating representative radiomic signatures, deep learning, and clinical features. Model performance was assessed by calculating the area under the receiver operating characteristic (ROC) curve. The established habitat radiomics features demonstrated encouraging performance in discriminating between EGFR mutant and wild-type, with predictive ability superior to other single models (AUC 0.886, 0.812, and 0.790 for the training, validation, and external test sets, respectively). The radiomics-based nomogram exhibited excellent performance, achieving the highest AUC values of 0.917, 0.837, and 0.809 in the training, validation, and external test sets, respectively. Decision curve analysis (DCA) indicated that the nomogram provided a higher net benefit than other radiomics models, offering valuable information for treatment.