Validation Set Research Articles

Permeability estimation for deformable porous media with convolutional neural network

Purpose Accurately evaluating fluid flow behaviors and determining permeability for deforming porous media is time-consuming and remains challenging. This paper aims to propose a novel machine-learning method for the rapid estimation of permeability of porous media at different deformation stages constrained by hydro-mechanical coupling analysis. Design/methodology/approach A convolutional neural network (CNN) is proposed in this paper, which is guided by the results of finite element coupling analysis of equilibrium equation for mechanical deformation and Boltzmann equation for fluid dynamics during the hydro-mechanical coupling process [denoted as Finite element lattice Boltzmann model (FELBM) in this paper]. The FELBM ensures the Lattice Boltzmann analysis of coupled fluid flow with an unstructured mesh, which varies with the corresponding nodal displacement resulting from mechanical deformation. It provides reliable label data for permeability estimation at different stages using CNN. Findings The proposed CNN can rapidly and accurately estimate the permeability of deformable porous media, significantly reducing processing time. The application studies demonstrate high accuracy in predicting the permeability of deformable porous media for both the test and validation sets. The corresponding correlation coefficients (R2) is 0.93 for the validation set, and the R2 for the test set A and test set B are 0.93 and 0.94, respectively. Originality/value This study proposes an innovative approach with the CNN to rapidly estimate permeability in porous media under dynamic deformations, guided by FELBM coupling analysis. The fast and accurate performance of CNN underscores its promising potential for future applications.

Automated quantification of avian influenza virus antigen in different organs

AbstractAs immunohistochemistry is valuable for determining tissue and cell tropism of avian influenza viruses (AIV), but time-consuming, an artificial intelligence-based workflow was developed to automate the AIV antigen quantification. Organ samples from experimental AIV infections including brain, heart, lung and spleen on one slide, and liver and kidney on another slide were stained for influenza A-matrixprotein and analyzed with QuPath: Random trees algorithms were trained to identify the organs on each slide, followed by threshold-based quantification of the immunoreactive area. The algorithms were trained and tested on two different slide sets, then retrained on both and validated on a third set. Except for the kidney, the best algorithms for organ selection correctly identified the largest proportion of the organ area. For most organs, the immunoreactive area assessed following organ selection was significantly and positively correlated to a manually assessed semiquantitative score. In the validation set, intravenously infected chickens showed a generally higher percentage of immunoreactive area than chickens infected oculonasally. Variability between the slide sets and a similar tissue texture of some organs limited the ability of the algorithms to select certain organs. Generally, suitable correlations of the immunoreactivity data results were achieved, facilitating high-throughput analysis of AIV tissue tropism.

Prediction of prostate cancer aggressiveness using magnetic resonance imaging radiomics: a dual-center study.

The Gleason score (GS) and positive needles are crucial aggressive indicators of prostate cancer (PCa). This study aimed to investigate the usefulness of magnetic resonance imaging (MRI) radiomics models in predicting GS and positive needles of systematic biopsy in PCa. A total of 218 patients with pathologically proven PCa were retrospectively recruited from 2 centers. Small-field-of-view high-resolution T2-weighted imaging and post-contrast delayed sequences were selected to extract radiomics features. Then, analysis of variance and recursive feature elimination were applied to remove redundant features. Radiomics models for predicting GS and positive needles were constructed based on MRI and various classifiers, including support vector machine, linear discriminant analysis, logistic regression (LR), and LR using the least absolute shrinkage and selection operator. The models were evaluated with the area under the curve (AUC) of the receiver-operating characteristic. The 11 features were chosen as the primary feature subset for the GS prediction, whereas the 5 features were chosen for positive needle prediction. LR was chosen as classifier to construct the radiomics models. For GS prediction, the AUC of the radiomics models was 0.811, 0.814, and 0.717 in the training, internal validation, and external validation sets, respectively. For positive needle prediction, the AUC was 0.806, 0.811, and 0.791 in the training, internal validation, and external validation sets, respectively. MRI radiomics models are suitable for predicting GS and positive needles of systematic biopsy in PCa. The models can be used to identify aggressive PCa using a noninvasive, repeatable, and accurate diagnostic method.

Efficacy of Random Forest Models in Predicting Multidrug-Resistant Gram-Negative Bacterial Nosocomial Infections Compared to Traditional Logistic Regression Models.

This study evaluates whether random forest (RF) models are as effective as traditional Logistic Regression (LR) models in predicting multidrug-resistant Gram-negative bacterial nosocomial infections. Data were collected from 541 patients with hospital-acquired Gram-negative bacterial infections at two tertiary-level hospitals in Urumqi, Xinjiang, China, from August 2022 to November 2023. Relevant literature informed the selection of significant predictors based on patients' pre-infection clinical information and medication history. The data were split into a training set of 379 cases and a validation set of 162 cases, adhering to a 7:3 ratio. Both RF and LR models were developed using the training set and subsequently evaluated on the validation set. The LR model achieved an accuracy of 84.57%, sensitivity of 82.89%, specificity of 80.10%, positive predictive value of 84%, negative predictive value of 85.06%, and a Yoden index of 0.69. In contrast, the RF model demonstrated superior performance with an accuracy of 89.51%, sensitivity of 90.79%, specificity of 88.37%, positive predictive value of 87.34%, negative predictive value of 91.57%, and a Yoden index of 0.79. Receiver operating characteristic curve analysis revealed an area under the curve of 0.91 for the LR model and 0.94 for the RF model. These findings indicate that the RF model surpasses the LR model in specificity, sensitivity, and accuracy in predicting hospital-acquired multidrug-resistant Gram-negative infections, showcasing its greater potential for clinical application.

Risk factors, prognostic factors, and nomograms for distant metastasis in patients with diagnosed duodenal cancer: A population-based study

BACKGROUND Duodenal cancer is one of the most common subtypes of small intestinal cancer, and distant metastasis (DM) in this type of cancer still leads to poor prognosis. Although nomograms have recently been used in tumor areas, no studies have focused on the diagnostic and prognostic evaluation of DM in patients with primary duodenal cancer. AIM To develop and evaluate nomograms for predicting the risk of DM and personalized prognosis in patients with duodenal cancer. METHODS Data on duodenal cancer patients diagnosed between 2010 and 2019 were extracted from the Surveillance, Epidemiology, and End Results database. Univariate and multivariate logistic regression analyses were used to identify independent risk factors for DM in patients with duodenal cancer, and univariate and multivariate Cox proportional hazards regression analyses were used to determine independent prognostic factors in duodenal cancer patients with DM. Two novel nomograms were established, and the results were evaluated by receiver operating characteristic (ROC) curves, calibration curves, and decision curve analysis (DCA). RESULTS A total of 2603 patients with duodenal cancer were included, of whom 457 cases (17.56%) had DM at the time of diagnosis. Logistic analysis revealed independent risk factors for DM in duodenal cancer patients, including gender, grade, tumor size, T stage, and N stage (P < 0.05). Univariate and multivariate COX analyses further identified independent prognostic factors for duodenal cancer patients with DM, including age, histological type, T stage, tumor grade, tumor size, bone metastasis, chemotherapy, and surgery (P < 0.05). The accuracy of the nomograms was validated in the training set, validation set, and expanded testing set using ROC curves, calibration curves, and DCA curves. The results of Kaplan-Meier survival curves (P < 0.001) indicated that both nomograms accurately predicted the occurrence and prognosis of DM in patients with duodenal cancer. CONCLUSION The two nomograms are expected as effective tools for predicting DM risk in duodenal cancer patients and offering personalized prognosis predictions for those with DM, potentially enhancing clinical decision-making.

Generative adversarial network-based synthesis of contrast-enhanced MR images from precontrast images for predicting histological characteristics in breast cancer

Objective. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a sensitive tool for assessing breast cancer by analyzing tumor blood flow, but it requires gadolinium-based contrast agents, which carry risks such as brain retention and astrocyte migration. Contrast-free MRI is thus preferable for patients with renal impairment or who are pregnant. This study aimed to investigate the feasibility of generating contrast-enhanced MR images from precontrast images and to evaluate the potential use of synthetic images in diagnosing breast cancer. Approach. This retrospective study included 322 women with invasive breast cancer who underwent preoperative DCE-MRI. A generative adversarial network (GAN) based postcontrast image synthesis (GANPIS) model with perceptual loss was proposed to generate contrast-enhanced MR images from precontrast images. The quality of the synthesized images was evaluated using the peak signal-to-noise ratio (PSNR) and structural similarity (SSIM). The diagnostic performance of the generated images was assessed using a convolutional neural network to predict Ki-67, luminal A and histological grade with the area under the receiver operating characteristic curve (AUC). The patients were divided into training (n = 200), validation (n = 60), and testing sets (n = 62). Main results. Quantitative analysis revealed strong agreement between the generated and real postcontrast images in the test set, with PSNR and SSIM values of 36.210 ± 2.670 and 0.988 ± 0.006, respectively. The generated postcontrast images achieved AUCs of 0.918 ± 0.018, 0.842 ± 0.028 and 0.815 ± 0.019 for predicting the Ki-67 expression level, histological grade, and luminal A subtype, respectively. These results showed a significant improvement compared to the use of precontrast images alone, which achieved AUCs of 0.764 ± 0.031, 0.741 ± 0.035, and 0.797 ± 0.021, respectively. Significance. This study proposed a GAN-based MR image synthesis method for breast cancer that aims to generate postcontrast images from precontrast images, allowing the use of contrast-free images to simulate kinetic features for improved diagnosis.

Identification and validation of aging-related genes in heart failure based on multiple machine learning algorithms

BackgroundIn the face of continued growth in the elderly population, the need to understand and combat age-related cardiac decline becomes even more urgent, requiring us to uncover new pathological and cardioprotective pathways.MethodsWe obtained the aging-related genes of heart failure through WGCNA and CellAge database. We elucidated the biological functions and signaling pathways involved in heart failure and aging through GO and KEGG enrichment analysis. We used three machine learning algorithms: LASSO, RF and SVM-RFE to further screen the aging-related genes of heart failure, and fitted and verified them through a variety of machine learning algorithms. We searched for drugs to treat age-related heart failure through the DSigDB database. Finally, We use CIBERSORT to complete immune infiltration analysis of aging samples.ResultsWe obtained 57 up-regulated and 195 down-regulated aging-related genes in heart failure through WGCNA and CellAge databases. GO and KEGG enrichment analysis showed that aging-related genes are mainly involved in mechanisms such as Cellular senescence and Cell cycle. We further screened aging-related genes through machine learning and obtained 14 key genes. We verified the results on the test set and 2 external validation sets using 15 machine learning algorithm models and 207 combinations, and the highest accuracy was 0.911. Through screening of the DSigDB database, we believe that rimonabant and lovastatin have the potential to delay aging and protect the heart. The results of immune infiltration analysis showed that there were significant differences between Macrophages M2 and T cells CD8 in aging myocardium.ConclusionWe identified aging signature genes and potential therapeutic drugs for heart failure through bioinformatics and multiple machine learning algorithms, providing new ideas for studying the mechanism and treatment of age-related cardiac decline.

Development and performance assessment of novel machine learning models for predicting postoperative pneumonia in aneurysmal subarachnoid hemorrhage patients: external validation in MIMIC-IV

BackgroundPostoperative pneumonia (POP) is one of the primary complications after aneurysmal subarachnoid hemorrhage (aSAH) and is associated with postoperative mortality, extended hospital stay, and increased medical fee. Early identification of pneumonia and more aggressive treatment can improve patient outcomes. We aimed to develop a model to predict POP in aSAH patients using machine learning (ML) methods.MethodsThis internal cohort study included 706 patients with aSAH undergoing intracranial aneurysm embolization or aneurysm clipping. The cohort was randomly split into a train set (80%) and a testing set (20%). Perioperative information was collected from participants to establish 6 machine learning models for predicting POP after surgical treatment. The area under the receiver operating characteristic curve (AUC), precision-recall curve were used to assess the accuracy, discriminative power, and clinical validity of the predictions. The final model was validated using an external validation set of 97 samples from the Medical Information Mart for Intensive Care IV (MIMIC-IV) database.ResultsIn this study, 15.01% of patients in the training set and 12.06% in the testing set with POP after underwent surgery. Multivariate logistic regression analysis showed that mechanical ventilation time (MVT), Glasgow Coma Scale (GCS), Smoking history, albumin level, neutrophil-to-albumin Ratio (NAR), c-reactive protein (CRP)-to-albumin ratio (CAR) were independent predictors of POP. The logistic regression (LR) model presented significantly better predictive performance (AUC: 0.91) than other models and also performed well in the external validation set (AUC: 0.89).ConclusionA machine learning model for predicting POP in aSAH patients was successfully developed using a machine learning algorithm based on six perioperative variables, which could guide high-risk POP patients to take appropriate preventive measures.

Development and validation of an MRI-Based nomogram to predict the effectiveness of immunotherapy for brain metastasis in patients with non-small cell lung cancer

IntroductionThe variability and unpredictability of immune checkpoint inhibitors (ICIs) in treating brain metastases (BMs) in patients with advanced non-small cell lung cancer (NSCLC) is the main concern. We assessed the utility of novel imaging biomarkers (radiomics) for discerning patients with NSCLC and BMs who would derive advantages from ICIs treatment.MethodsData clinical outcomes and pretreatment magnetic resonance images (MRI) were collected on patients with NSCLC with BMs treated with ICIs between June 2019 and June 2022 and divided into training and test sets. Metastatic brain lesions were contoured using ITK-SNAP software, and 3748 radiomic features capturing both intra- and peritumoral texture patterns were extracted. A clinical radiomic nomogram (CRN) was built to evaluate intracranial progression-free survival, progression-free survival, and overall survival. The prognostic value of the CRN was assessed by Kaplan–Meier survival analysis and log-rank tests.ResultsIn the study, a total of 174 patients were included, and 122 and 52 were allocated to the training and validation sets correspondingly. The intratumoral radiomic signature, peritumoral radiomic signature, clinical signature, and CRN predicted intracranial objective response rate. Kaplan–Meier analyses showed a significantly longer intracranial progression-free survival in the low-CRN group than in the high-CRN group (p < 0.001). The CRN was also significantly associated with progression-free survival (p < 0.001) but not overall survival.DiscussionRadiomics biomarkers from pretreatment MRI images were predictive of intracranial response. Pretreatment radiomics may allow the early prediction of benefits.

Multi-feature, Chinese-Western medicine-integrated prediction model for diabetic peripheral neuropathy based on machine learning and SHAP.

Clinical studies have shown that diabetic peripheral neuropathy (DPN) has been on the rise, with most patients presenting with severe and progressive symptoms. Currently, most of the available prediction models for DPN are derived from general clinical information and laboratory indicators. Several Traditional Chinese medicine (TCM) indicators have been utilised to construct prediction models. In this study, we established a novel machine learning-based multi-featured Chinese-Western medicine-integrated prediction model for DPN using clinical features of TCM. The clinical data of 1581 patients with Type 2 diabetes mellitus (T2DM) treated at the Department of Endocrinology of the First Affiliated Hospital of Anhui University of Chinese Medicine were collected. The data (including general information, laboratory parameters and TCM features) of 1142 patients with T2DM were selected after data cleaning. After baseline description analysis of the variables, the data were divided into training and validation sets. Four prediction models were established and their performance was evaluated using validation sets. Meanwhile, the accuracy, precision, recall, F1 score and area under the curve (AUC) of ROC were calculated using ten-fold cross-validation to further assess the performance of the models. An explanatory analysis of the results of the DPN prediction model was carried out using the SHAP framework based on machine learning-based prediction models. Of the 1142 patients with T2DM, 681 had a comorbidity of DPN, while 461 did not. There was a significant difference between the two groups in terms of age, cause of disease, systolic pressure, HbA1c, ALT, RBC, Cr, BUN, red blood cells in the urine, glucose in the urine, and protein in the urine (p<0.05). T2DM patients with a comorbidity of DPN exhibited diverse TCM symptoms, including limb numbness, limb pain, hypodynamia, thirst with desire for drinks, dry mouth and throat, blurred vision, gloomy complexion, and unsmooth pulse, with statistically significant differences (p<0.05). Our results showed that the proposed multi-featured Chinese-Western medicine-integrated prediction model was superior to conventional models without characteristic TCM indicators. The model showed the best performance (accuracy=0.8109, precision=0.8029, recall=0.9060, F1 score=0.8511, and AUC=0.9002). SHAP analysis revealed that the dominant risk factors that caused DPN were TCM symptoms (limb numbness, thirst with desire for drinks, blurred vision), age, cause of disease, and glycosylated haemoglobin. These risk factors were exerted positive effects on the DPN prediction models. A multi-feature, Chinese-Western medicine-integrated prediction model for DPN was established and validated. The model improves early-stage identification of high-risk groups for DPN in the diagnosis and treatment of T2DM, while also providing informative support for the intelligent management of chronic conditions such as diabetes.

Predictive Modeling and Experimental Validation for Assessing the Mechanical Properties of Cementitious Composites Made with Silica Fume and Ground Granulated Blast Furnace Slag

Using sustainable cement-based alternatives, such as secondary cementitious raw materials (SCMs), could be a viable option to decrease CO2 emissions resulting from cement production. Previously conducted studies to determine the optimal mix designs of concrete primarily focused on either experimental approaches or empirical modeling techniques. However, in these experimental approaches, few tests could be performed for optimization due to time restrictions and lack of resources, and empirical modeling methods cannot be relied on without external validation. The machine learning-based approaches are further characterized by certain shortcomings, including a smaller number of data points, a less robust connection among the controlling factors, and a lack of comparative analyses among machine learning models. Furthermore, the literature on predicting the performance of concrete utilizing binary SCMs (silica fume (SF) and ground granulated blast furnace slag (GGBS)) is not available. Therefore, to address these drawbacks, this research aimed to integrate ML-based models with experimental validations for accurate predictions of the compressive strength (CS) and tensile strength (TS) of concrete that includes SF and GGBS as SCMs. Three soft computing techniques, namely the ANN, ANFIS, and GEP methods, were used for prediction purposes. Eight major input parameters, including the W/B ratio, cement, GGBS, SF, coarse aggregates, fine aggregates, superplasticizer, and the age of the specimens, were considered for modeling. The validity of the established models was assessed by using external experimental validation criteria, statistical metrics, and performance measures. In addition, sensitivity and parametric analyses were performed. Based on statistical measures, the ANFIS models outperformed other models with higher correlation and lower statistical error values. However, the GEP models exhibited superior performance compared to ANFIS and ANN with respect to the closeness of the RMSE, MAE, RSE, and R2 values between the training, validation, and testing sets for both the CS and TS models. Experimental validation showed strong evidence for the applicability of the proposed models with an R2 of 0.88 and error percentages of less than 10%. Sensitivity and parametric investigations demonstrated that the input variables exhibited the patterns described in the experimental dataset and the available literature. Hence, the proposed models are accurate, have better prediction performance, and can be used for design purposes.

Automatic Segmentation of Bone Marrow Lesions on MRI Using a Deep Learning Method

Bone marrow lesion (BML) volume is a potential biomarker of knee osteoarthritis (KOA) as it is associated with cartilage degeneration and pain. However, segmenting and quantifying the BML volume is challenging due to the small size, low contrast, and various positions where the BML may occur. It is also time-consuming to delineate BMLs manually. In this paper, we proposed a fully automatic segmentation method for BMLs without requiring human intervention. The model takes intermediate weighted fat-suppressed (IWFS) magnetic resonance (MR) images as input, and the output BML masks are evaluated using both regular 2D Dice similarity coefficient (DSC) of the slice-level area metric and 3D DSC of the subject-level volume metric. On a dataset with 300 subjects, each subject has a sequence of 36 IWFS MR images approximately. We randomly separated the dataset into training, validation, and testing sets with a 70%/15%/15% split at the subject level. Since not every subject or image has a BML, we excluded the images without a BML in each subset. The ground truth of the BML was labeled by trained medical staff using a semi-automatic tool. Compared with the ground truth, the proposed segmentation method achieved a Pearson’s correlation coefficient of 0.98 between the manually measured volumes and automatically segmented volumes, a 2D DSC of 0.68, and a 3D DSC of 0.60 on the testing set. Although the DSC result is not high, the high correlation of 0.98 indicates that the automatically measured BML volume is strongly correlated with the manually measured BML volume, which shows the potential to use the proposed method as an automatic measurement tool for the BML biomarker to facilitate the assessment of knee OA progression.

A novel electronic health record-based, machine-learning model to predict severe hypoglycemia leading to hospitalizations in older adults with diabetes: A territory-wide cohort and modeling study.

Older adults with diabetes are at high risk of severe hypoglycemia (SH). Many machine-learning (ML) models predict short-term hypoglycemia are not specific for older adults and show poor precision-recall. We aimed to develop a multidimensional, electronic health record (EHR)-based ML model to predict one-year risk of SH requiring hospitalization in older adults with diabetes. We adopted a case-control design for a retrospective territory-wide cohort of 1,456,618 records from 364,863 unique older adults (age ≥65 years) with diabetes and at least 1 Hong Kong Hospital Authority attendance from 2013 to 2018. We used 258 predictors including demographics, admissions, diagnoses, medications, and routine laboratory tests in a one-year period to predict SH events requiring hospitalization in the following 12 months. The cohort was randomly split into training, testing, and internal validation sets in a 7:2:1 ratio. Six ML algorithms were evaluated including logistic-regression, random forest, gradient boost machine, deep neural network (DNN), XGBoost, and Rulefit. We tested our model in a temporal validation cohort in the Hong Kong Diabetes Register with predictors defined in 2018 and outcome events defined in 2019. Predictive performance was assessed using area under the receiver operating characteristic curve (AUROC), area under the precision-recall curve (AUPRC) statistics, and positive predictive value (PPV). We identified 11,128 SH events requiring hospitalization during the observation periods. The XGBoost model yielded the best performance (AUROC = 0.978 [95% CI 0.972 to 0.984]; AUPRC = 0.670 [95% CI 0.652 to 0.688]; PPV = 0.721 [95% CI 0.703 to 0.739]). This was superior to an 11-variable conventional logistic-regression model comprised of age, sex, history of SH, hypertension, blood glucose, kidney function measurements, and use of oral glucose-lowering drugs (GLDs) (AUROC = 0.906; AUPRC = 0.085; PPV = 0.468). Top impactful predictors included non-use of lipid-regulating drugs, in-patient admission, urgent emergency triage, insulin use, and history of SH. External validation in the HKDR cohort yielded AUROC of 0.856 [95% CI 0.838 to 0.873]. Main limitations of this study included limited transportability of the model and lack of geographically independent validation. Our novel-ML model demonstrated good discrimination and high precision in predicting one-year risk of SH requiring hospitalization. This may be integrated into EHR decision support systems for preemptive intervention in older adults at highest risk.

An Online Digital Imaging Excitation Sensor for Wind Turbine Gearbox Wear Condition Monitoring Based on Adaptive Deep Learning Method

This paper designed and developed an online digital imaging excitation sensor for wind power gearbox wear condition monitoring based on an adaptive deep learning method. A digital imaging excitation sensing image information collection architecture for magnetic particles in lubricating oil was established to characterize the wear condition of mechanical equipment, achieving the real-time online collection of wear particles in lubricating oil. On this basis, a mechanical equipment wear condition diagnosis method based on online wear particle images is proposed, obtaining data from an engineering test platform based on a wind power gearbox. Firstly, a foreground segmentation preprocessing method based on the U-Net network can effectively eliminate the interference of bubbles and dark fields in online wear particle images, providing high-quality segmentation results for subsequent image processing, A total of 1960 wear particle images were collected in the experiment, the average intersection union ratio of the validation set is 0.9299, and the accuracy of the validation set is 0.9799. Secondly, based on the foreground segmentation preprocessing of wear particle images, by using the watered algorithm to obtain the number of particles in each size segment, we obtained the number of magnetic particle grades in three different ranges: 4–38 µm, 39–70 µm, and &gt;70 µm. Thirdly, we proposed a method named multidimensional transformer (MTF) network. Mean Square Error (MSE), Root Mean Square Error (RMSE), and Mean Absolute Error (MAE) are used to obtain the error, and the maintenance strategy is formulated according to the predicted trend. The experimental results show that the predictive performance of our proposed model is better than that of LSTM and TCN. Finally, the online real-time monitoring system triggered three alarms, and at the same time, our offline sampling data analysis was conducted, the accuracy of online real-time monitoring alarms was verified, and the gearbox of the wind turbine was shut down for maintenance and repair.

Prediction of Acute Cardiac Rejection Based on Gene Expression Profiles

Acute cardiac rejection remains a significant challenge in the post-transplant period, necessitating meticulous monitoring and timely intervention to prevent graft failure. Thus, the goal of the present study was to identify novel biomarkers involved in acute cardiac rejection, paving the way for personalized diagnostic, preventive, and treatment strategies. A total of 809 differentially expressed genes were identified in the GSE150059 dataset. We intersected genes selected by analysis of variance, recursive feature elimination, least absolute shrinkage and selection operator, and random forest classifier to identify the most relevant genes involved in acute cardiac rejection. Thus, HCP5, KLRD1, GZMB, PLA1A, GNLY, and KLRB1 were used to train eight machine learning models: random forest, logistic regression, decision trees, support vector machines, gradient boosting machines, K-nearest neighbors, XGBoost, and neural networks. Models were trained, tested, and validated on the GSE150059 dataset (MMDx-based diagnosis of rejection). Eight algorithms achieved great performance in predicting acute cardiac rejection. However, all machine learning models demonstrated poor performance in two external validation sets that had rejection diagnosis based on histology: merged GSE2596 and GSE4470 dataset and GSE9377 dataset, thus highlighting differences between these two methods. According to SHAP and LIME, KLRD1 and HCP5 were the most impactful genes.

Science lab safety goes immersive: An ecological media-comparison study with gender analyses assessing iVR’s learning effectiveness

We conducted a media-comparison study in ecologically valid settings to understand immersive virtual reality’s (iVR’s) instructional effectiveness in a university science course. We tested how complementing regular science lab safety instruction with interactive iVR simulation, desktop simulation, or the re-viewing of a text-heavy manual compare with each other in terms of knowledge-related and affective learning outcomes. We also explored gender differences in the outcomes across these instructional conditions. 102 undergraduates (51 females) were randomly assigned to one of the instructional conditions. Throughout the one-day course, all students received the same set of instructions, demonstrations, and hands-on lab safety training except for the following: the iVR group engaged with HMD-based interactive lab safety iVR training simulation; the desktop group interacted with the same simulation on a laptop, whereas the remaining group re-viewed the text-heavy course material in detail. Topic knowledge-related and self-report affective data were collected before and immediately after the course. Statistical analyses revealed that: (i) all three instructional modes helped students gain significant lab safety knowledge, (ii) there were several significant between-group differences in multiple affective measures, and (iii) the instructional modes affected/benefited the two genders considerably differently. Besides extending previous findings, the strong ecological grounding of our results adds important insights into real-life implications of integrating different media in undergraduate education. Our gender-related findings merely scratch the surface on the complex issue of “designing for diversity”, inviting scaled-up efforts to develop more equitable technology-enhanced science learning settings to address the cognitive-affective needs of different genders and other diversities.

Acute Pancreatitis in Pregnancy: A Propensity Score Matching Analysis and Dynamic Nomogram for Risk Assessment.

Acute pancreatitis is easily confused with abdominal pain symptoms, and it could lead to serious complications for pregnant women and fetus, the mortality was as high as 3.3% and 11.6-18.7%, respectively. However, there is still lack of sensitive laboratory markers for early diagnosis of APIP and authoritative guidelines to guide treatment. The purpose of this study was to explore the risk factors of acute pancreatitis in pregnancy, establish, and evaluate the dynamic prediction model of risk factors in acute pancreatitis in pregnancy patients. Clinical data of APIP patients and non-pregnant acute pancreases patients who underwent regular antenatal check-ups during the same period were collected. The dataset after propensity matching was randomly divided into training set and verification set at a ratio of 7:3. The model was constructed using Logistic regression, least absolute shrinkage and selection operator regression, R language and other methods. The training set model was used to construct the diagnostic nomogram model and the validation set was used to validate the model. Finally, the accuracy and clinical practicability of the model were evaluated. A total of 111 APIP were included. In all APIP patients, hyperlipidemic pancreatitis was the most important reason. The levels of serum amylase, creatinine, albumin, triglyceride, high-density lipoprotein cholesterol, and apolipoprotein A1 were significantly different between the two groups. The propensity matching method was used to match pregnant pancreatitis patients and pregnant non-pancreatic patients 1:1 according to age and gestational age, and the matching tolerance was 0.02. The multivariate logistic regression analysis of training set showed that diabetes, triglyceride, Body Mass Index, white blood cell, and C-reactive protein were identified and entered the dynamic nomogram. The area under the ROC curve of the training set was 0.942 and in validation set was 0.842. The calibration curve showed good predictive in training set, and the calibration performance in the validation set was acceptable. The calibration curve showed the consistency between the nomogram model and the actual probability. The dynamic nomogram model we constructed to predict the risk factors of acute pancreatitis in pregnancy has high accuracy, discrimination, and clinical practicability.

Ensemble machine learning prediction of hyperuricemia based on a prospective health checkup population

Objectives: An accurate prediction model for hyperuricemia (HUA) in adults remain unavailable. This study aimed to develop a stacking ensemble prediction model for HUA to identify high-risk groups and explore risk factors.Methods: A prospective health checkup cohort of 40899 subjects was examined and randomly divided into the training and validation sets with the ratio of 7:3. LASSO regression was employed to screen out important features and then the ROSE sampling was used to handle the imbalanced classes. An ensemble model using stacking strategy was constructed based on three individual models, including support vector machine, decision tree C5.0, and eXtreme gradient boosting. Model validations were conducted using the area under the receiver operating characteristic curve (AUC) and the calibration curve, as well as metrics including accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1 score. A model agnostic instance level variable attributions technique (iBreakdown) was used to illustrate the black-box nature of our ensemble model, and to identify contributing risk factors.Results: Fifteen important features were screened out of 23 clinical variables. Our stacking ensemble model with an AUC of 0.854, outperformed the other three models, support vector machine, decision tree C5.0, and eXtreme gradient boosting with AUCs of 0.848, 0.851 and 0.849 respectively. Calibration accuracy as well as other metrics including accuracy, specificity, negative predictive value, and F1 score were also proved our ensemble model’s superiority. The contributing risk factors were estimated using six randomly selected subjects, which showed that being female and relatively younger, together with having higher baseline uric acid, body mass index, γ-glutamyl transpeptidase, total protein, triglycerides, creatinine, and fasting blood glucose can increase the risk of HUA. To further validate our model’s applicability in the health checkup population, we used another cohort of 8559 subjects that also showed our ensemble prediction model had favorable performances with an AUC of 0.846.Conclusion: In this study, the stacking ensemble prediction model for HUA was developed, and it outperformed three individual models that compose it (support vector machine, decision tree C5.0, and eXtreme gradient boosting). The contributing risk factors were identified with insightful ideas.

Identification of Multiclass Pediatric Low-Grade Neuroepithelial Tumor Molecular Subtype with ADC MR Imaging and Machine Learning.

Molecular biomarker identification increasingly influences the treatment planning of pediatric low-grade neuroepithelial tumors (PLGNTs). We aimed to develop and validate a radiomics-based ADC signature predictive of the molecular status of PLGNTs. In this retrospective bi-institutional study, we searched the PACS for baseline brain MRIs from children with PLGNTs. Semiautomated tumor segmentation on ADC maps was performed using the semiautomated level tracing effect tool with 3D Slicer. Clinical variables, including age, sex, and tumor location, were collected from chart review. The molecular status of tumors was derived from biopsy. Multiclass random forests were used to predict the molecular status and fine-tuned using a grid search on the validation sets. Models were evaluated using independent and unseen test sets based on the combined data, and the area under the receiver operating characteristic curve (AUC) was calculated for the prediction of 3 classes: KIAA1549-BRAF fusion, BRAF V600E mutation, and non-BRAF cohorts. Experiments were repeated 100 times using different random data splits and model initializations to ensure reproducible results. Two hundred ninety-nine children from the first institution and 23 children from the second institution were included (53.6% male; mean, age 8.01 years; 51.8% supratentorial; 52.2% with KIAA1549-BRAF fusion). For the 3-class prediction using radiomics features only, the average test AUC was 0.74 (95% CI, 0.73-0.75), and using clinical features only, the average test AUC was 0.67 (95% CI, 0.66-0.68). The combination of both radiomics and clinical features improved the AUC to 0.77 (95% CI, 0.75-0.77). The diagnostic performance of the per-class test AUC was higher in identifying KIAA1549-BRAF fusion tumors among the other subgroups (AUC = 0.81 for the combined radiomics and clinical features versus 0.75 and 0.74 for BRAF V600E mutation and non-BRAF, respectively). ADC values of tumor segmentations have differentiative signals that can be used for training machine learning classifiers for molecular biomarker identification of PLGNTs. ADC-based pretherapeutic differentiation of the BRAF status of PLGNTs has the potential to avoid invasive tumor biopsy and enable earlier initiation of targeted therapy.

A CT-based radiomics nomogram for predicting histologic grade and outcome in chondrosarcoma

ObjectiveThe preoperative identification of tumor grade in chondrosarcoma (CS) is crucial for devising effective treatment strategies and predicting outcomes. The study aims to build and validate a CT-based radiomics nomogram (RN) for the preoperative identification of tumor grade in CS, and to evaluate the correlation between the RN-predicted tumor grade and postoperative outcome.MethodsA total of 196 patients (139 in the training cohort and 57 in the external validation cohort) were derived from three different centers. A clinical model, radiomics signature (RS) and RN (which combines significant clinical factors and RS) were developed and validated to assess their ability to distinguish low-grade from high-grade CS with area under the curve (AUC). Additionally, Kaplan-Meier survival analysis was applied to examine the association between RN-predicted tumor grade and recurrence-free survival (RFS) of CS. The predictive accuracy of the RN was evaluated using Harrell’s concordance index (C-index), hazard ratio (HR) and AUC.ResultsSize, endosteal scalloping and active periostitis were selected to build the clinical model. Three radiomics features, based on CT images, were selected to construct the RS. Both the RN (AUC, 0.842) and RS (AUC, 0.835) were superior to the clinical model (AUC, 0.776) in the validation set (P = 0.003, 0.040, respectively). A correlation between Nomogram score (Nomo-score, derived from RN) and RFS was observed through Kaplan-Meier survival analysis in the training and test cohorts (log-rank P < 0.050). Patients with high Nomo-score tumors were 2.669 times more likely to suffer recurrence than those with low Nomo-score tumors (HR, 2.669, P < 0.001).ConclusionsThe CT-based RN performed well in predicting both the histologic grade and outcome of CS.