External Validation Set Research Articles

Predictive value of contrast-enhanced MRI for the regrowth of residual uterine fibroids after high-intensity focused ultrasound treatment.

To investigate whether the signal intensity (SI) ratio of residual fibroid (RF) to myometrium using Contrast-Enhanced Magnetic Resonance Imaging (CE-MRI) could predict fibroid regrowth after high-intensity focused ultrasound (HIFU) treatment. A retrospective analysis was conducted among 164 patients with uterine fibroids who underwent HIFU. To predict the RF regrowth, the SI perfusion parameters were quantified using the RF-myometrium SI ratio on CE-MRI on day 1 post-HIFU and then compared with the fibroid-myometrium SI ratio on the T2-weighted image (T2WI) and Funaki classification 1 year later. Thirty cases from another center were used as an external validation set to evaluate the performance of RF-myometrium SI ratio. The predictive performance of the RF-myometrium SI ratio on CE-MRI on day 1 post-HIFU (Area Under Curve, AUC: 0.869) was superior to that of the preoperative and postoperative fibroid-myometrium SI ratios on the T2WI (AUC: 0.724, 0.696) and Funaki classification (AUC: 0.663, 0.623). Multivariate analysis showed that the RF- myometrium SI ratio and RF thickness were independent factors. The RF-myometrium SI ratio reflects the long-term rate of re-intervention (r = 0.455, p < 0.001). The RF-myometrium SI ratio on CE-MRI exhibits greater accuracy in predicting RF regrowth compared to the SI classification and the SI ratio on T2WI. The ratio of residual uterine fibroid to myometrial signal intensity on contrast-enhanced (CE)-MRI can reflect residual blood supply, predict regrowth of fibroids, and thus reflect long-term re-intervention rate and recovery situation of clinical high-intensity focused ultrasound (HIFU) treatment. Contrast-enhanced (CE)-MRI can indicate the blood supply of residual uterine fibroids after high-intensity focused ultrasound (HIFU) treatment. The predictive capability of CE-MRI ratio surpasses T2WI ratio and the Funaki. Residual fibroids can serve as a measure of the long-term efficacy of HIFU.

Evaluation of the GATIS score for predicting prognosis in rectal neuroendocrine neoplasms

The GATIS score, developed by Zeng et al , represents a significant advancement in predicting the prognosis of patients with rectal neuroendocrine neoplasms (R-NENs). This study, which included 1408 patients from 17 major medical centres in China over 12 years, introduces a novel prognostic model based on the tumour grade, T stage, tumour size, age, and the prognostic nutritional index. Compared with traditional methods such as the World Health Organization classification and TNM staging systems, the GATIS score has superior predictive power for overall survival and progression-free survival. With a C-index of 0.915 in the training set and 0.812 in the external validation set, the GATIS score’s robustness and reliability are evident. The study’s use of a large, multi-centre cohort and rigorous validation processes underscore its significance. The GATIS score offers clinicians a powerful tool to accurately predict patient outcomes, guide treatment decisions, and improve follow-up strategies. This development represents a crucial step forwards in the management of R-NENs, addressing the complexity and variability of these tumours and setting a new benchmark for future research and clinical practice.

An AI-driven preoperative radiomic subtype for predicting the prognosis and treatment response of patients with papillary thyroid carcinoma.

8-28% of Papillary thyroid carcinoma (PTC) experience recurrence, complicating risk stratification and treatment. We previously identified an inflammatory molecular subtype of PTC associated with poor prognosis. Based on this subtype, we aimed to develop and validate a noninvasive radiomic signature to predict prognosis and treatment response in PTC patients. We collected preoperative ultrasound images from two large independent centers (n=2506) to develop and validate a Deep Learning Radiomics signature of Inflammation (DLRI) for predicting the inflammatory subtype of PTC, including its correlation with prognosis and anti-inflammatory traditional Chinese medicine (TCM) treatment. Training set 1 (n=64) and internal validation set 2 (n=1108) were from Tianjin Medical University Cancer Institute and Hospital. External validation set 1 (n=76) and 2 (n=1258) were from Fudan University Shanghai Cancer Center. We developed DLRI to accurately predict PTC's inflammatory subtype (AUC=0.97 in the training set 1 and AUC=0.82 in the external validation set 1). High-risk DLRI was significantly associated with poor disease-free survival in the first cohort (HR=16.49, 95% CI: 7.92-34.35, P<0.001) and second cohort (HR=5.42, 95%: 3.67-8.02, P<0.001). DLRI independently predicted disease-free survival, irrespective of clinicopathological variables (P<0.001 for all). Furthermore, patients with high-risk DLRI were likely to benefit from anti-inflammatory TCM treatment (HR=0.19, 95% CI: 0.06-0.55, P=0.002), whereas those in low-risk DLRI did not. DLRI is a reliable noninvasive tool for evaluating prognosis and guiding anti-inflammatory TCM treatment in PTC patients. Prospective studies are needed to confirm these findings.

A Comprehensive Quality Evaluation for Gentiana Rigescens Franch. by Fingerprinting Combined with Chemometrics and Network Pharmacology.

Gentiana rigescens Franch. (G. rigescens) is a unique traditional medicinal herb from southwestern China, and its clinical mechanism for the treatment of hepatitis and the quality differences between different origins are not clear. The research aims to analyze the mechanisms for the treatment of hepatitis and differences in inter-origin differences using analytical techniques, chemometrics, and network pharmacology. Through infrared spectroscopy, spectral images, and high-performance liquid chromatography (HPLC) analysis, it was found that there were differences in absorbance intensity and significant differences in compound content among the samples' origin. G. rigescens iridoids and flavonoids exert therapeutic effects on hepatitis through multiple targets (GAPDH, EGFR, and MMP9, etc.) and multiple pathways (non-small cell lung cancer, hepatitis C, etc.). The above HPLC, chemometrics, and network pharmacology results revealed that gentiopicroside, and swertiamarine was the best quality marker among origins. The accuracy of the ResNet model train, test, and external validation sets for synchronous spectral images were 100 %, which could be utilized as an effective tool for tracing G. rigescens's origins. The R2 of the calibration and validation sets of the PLSR model was higher than 0.70. This model had excellent predictive performance in determining the content of gentiopicroside and swertiamarine, and could quickly, accurately, and effectively predict these two compounds. The research investigates the differences in G. rigescens origins from multiple perspectives, establishes image recognition models and prediction models, and provides new methods and theoretical basis for quality control of G. rigescens.

Development and validation of a nomogram to predict the survival and estimate surgical benefits for gastric cancer with liver metastasis receiving primary tumor resection

BackgroundSurgical treatment has been widely controversial for gastric cancer accompanied by liver metastasis (GCLM). This paper aims to develop and validate a nomogram to predict the survival and estimate surgical benefits for GCLM patients.MethodsA total of 616 GCLM patients from the Surveillance, Epidemiology, and End Results Program (SEER) database and 74 GCLM patients receiving primary tumor resection (PTR) from the Chinese center were included in this study. Patients from the SEER database were divided into training set (with PTR) (n=493) and non-operative set (without PTR) (n=123). Patients undergoing PTR from China were included as external validation set. Independent risk factors associated with the overall survival of GCLM patients undergoing PTR were identified in the training set via log-rank test and Cox regression analysis. Afterwards, a comprehensive model and corresponding nomogram were constructed and validated by validation set.ResultsThe survival of patients undergoing PTR (n=493) was longer than that without PTR (n=123) (log-rank test, p&amp;lt;0.0001) in SEER cohort. T stage (HR=1.40, 95% CI=1.14, 1.73), differentiation grade (HR=1.47, 95% CI=1.17, 1.85), non-hepatic metastases (HR=1.69, 95% CI=1.29, 2.21), and adjuvant therapy (HR=0.34, 95% CI= 0.28, 0.42) were closely related with the survival of GCLM with PTR, and thus, a four-factor nomogram was established. However, GCLM patients receiving PTR in the high-risk subgroup (n=255) screened out by the nomogram did not have better survival outcomes compared with patients without PTR (n=123) (log-rank test, p=0.25).ConclusionsThe nomogram could predict survival of GCLM patients receiving PTR with acceptable accuracy. In addition, although PTR did improve the survival of whole GCLM patients, patients in the high-risk subgroup were unable to benefit from PTR, which could assist clinicians to make decisions for the treatment of GCLM.

Development and external validation of an interpretable machine learning model for the prediction of intubation in the intensive care unit

Given the limited capacity to accurately determine the necessity for intubation in intensive care unit settings, this study aimed to develop and externally validate an interpretable machine learning model capable of predicting the need for intubation among ICU patients. Seven widely used machine learning (ML) algorithms were employed to construct the prediction models. Adult patients from the Medical Information Mart for Intensive Care IV database who stayed in the ICU for longer than 24 h were included in the development and internal validation. The model was subsequently externally validated using the eICU-CRD database. In addition, the SHapley Additive exPlanations method was employed to interpret the influence of individual parameters on the predictions made by the model. A total of 11,988 patients were included in the final cohort for this study. The CatBoost model demonstrated the best performance (AUC: 0.881). In the external validation set, the efficacy of our model was also confirmed (AUC: 0.750), which suggests robust generalization capabilities. The Glasgow Coma Scale (GCS), body mass index (BMI), arterial partial pressure of oxygen (PaO2), respiratory rate (RR) and length of stay (LOS) before ICU were the top 5 features of the CatBoost model with the greatest impact. We developed an externally validated CatBoost model that accurately predicts the need for intubation in ICU patients within 24 to 96 h of admission, facilitating clinical decision-making and has the potential to improve patient outcomes. The prediction model utilizes readily obtainable monitoring parameters and integrates the SHAP method to enhance interpretability, providing clinicians with clear insights into the factors influencing predictions.

NIR spectroscopy prediction model for capsaicin content estimation in chilli: A rapid mining tool for trait-specific germplasm screening

Chilli is a widely produced crop, highly valued for its capsaicin content, a key economic trait. Traditional wet chemistry methods for estimating capsaicin are time-taking and laborious, while non-destructive methods like NIRS coupled with chemometrics, offer efficient alternatives, simplifying and accelerating biochemical assessments. This study is the first to develop and validate and tested for applicability of NIRS-based prediction model for capsaicin content in Indian chilli germplasm using MPLS regression. Various mathematical treatments were performed, and the most suited model was selected based on high RSQexternal, RPD and lower SEP values in the external validation set, indicating strong prediction accuracy and minimal error. The model achieved high RSQexternal value of 0.808, RPD value of 2.088 and low SEP value of 3.415 for capsaicin content, demonstrating excellent prediction performance. A paired sample t-test p-value of 0.757 (p > 0.05) showed non-significant difference between wet lab and predicted values, confirming the model’s accuracy. The applicability of the model was validated on fresh harvest germplasm the following year, showing a higher reliability score of 0.949, further confirming model’s reliability. This model would aid in high-throughput, accurate screening of chilli germplasm for capsaicin, accelerating chilli crop improvement programs and the development of new high-capsaicin varieties.

Development of a Dual-Plane MRI-Based Deep Learning Model to Assess the 1-Year Postoperative Outcomes in Lumbar Disc Herniation After Tubular Microdiscectomy.

Tubular microdiscectomy (TMD) is a treatment for lumbar disc herniation (LDH). Although the combination of MRI and deep learning (DL) has shown promise, its application in evaluating postoperative outcomes in TMD has not been fully explored. To evaluate whether integrating preoperative dual-plane MRI-based DL features with clinical features can assess 1-year outcomes in TMD for LDH. Retrospective. The study involved 548 patients who underwent TMD between January 2016 and January 2021. Training set (N = 305, mean age 51.85 ± 13.84 years, 56.4% male). Internal validation set (N = 131, mean age 51.85 ± 13.84 years, 54.2% male). External validation set (N = 112, mean age 51.54 ± 14.43 years, 50.9% male). 3 T MRI with sagittal and transverse T2-weighted sequences (Fast Spin Echo). Ground truth labels were based on improvement rate in 1-year Japanese Orthopaedic Association (JOA) scores. Information on 42 preoperative clinical features was collected. The largest protrusions were identified from T2 MRI by three clinicians and were used to train deep learning models (ResNet50, ResNet101, and ResNet152) to extract DL features. After feature selection, three models were built, namely, clinical, DL, and combined models. Chi-square or Fisher's exact tests was used for group comparisons. Quantitative differences were analyzed using the t-test or Mann-Whitney U test. P-values <0.05 were considered significant. Models were validated on internal and external datasets using metrics such as the area under the curve (AUC). The AUCs of the clinical models achieved 0.806 (internal) and 0.779 (external). ResNet152 performed best in three DL models, with AUCs of 0.858 (internal) and 0.834 (external). The combined model achieved AUCs of 0.889 (internal) and 0.857 (external). A model combining preoperative dual-plane MRI DL features and clinical features can assess 1-year outcomes of TMD for LDH. 4 TECHNICAL EFFICACY: Stage 2.

A generalised computer vision model for improved glaucoma screening using fundus images.

Worldwide, glaucoma is a leading cause of irreversible blindness. Timely detection is paramount yet challenging, particularly in resource-limited settings. A novel, computer vision-based model for glaucoma screening using fundus images could enhance early and accurate disease detection. To develop and validate a generalised deep-learning-based algorithm for screening glaucoma using fundus image. The glaucomatous fundus data were collected from 20 publicly accessible databases worldwide, resulting in 18,468 images from multiple clinical settings, of which 10,900 were classified as healthy and 7568 as glaucoma. All the data were evaluated and downsized to fit the model's input requirements. The potential model was selected from 20 pre-trained models and trained on the whole dataset except Drishti-GS. The best-performing model was further trained to classify healthy and glaucomatous fundus images using Fastai and PyTorch libraries. The model's performance was compared against the actual class using the area under the receiver operating characteristic (AUROC), sensitivity, specificity, accuracy, precision and the F1-score. The high discriminative ability of the best-performing model was evaluated on a dataset comprising 1364 glaucomatous discs and 2047 healthy discs. The model reflected robust performance metrics, with an AUROC of 0.9920 (95% CI: 0.9920-0.9921) for both the glaucoma and healthy classes. The sensitivity, specificity, accuracy, precision, recall and F1-scores were consistently higher than 0.9530 for both classes. The model performed well on an external validation set of the Drishti-GS dataset, with an AUROC of 0.8751 and an accuracy of 0.8713. This study demonstrated the high efficacy of our classification model in distinguishing between glaucomatous and healthy discs. However, the model's accuracy slightly dropped when evaluated on unseen data, indicating potential inconsistencies among the datasets-the model needs to be refined and validated on larger, more diverse datasets to ensure reliability and generalisability. Despite this, our model can be utilised for screening glaucoma at the population level.

Development and validation of a nomogram diagnostic model for coronary slow flow patients: A cross-sectional study.

In this study, risk factors for coronary slow flow (CSF) patients were examined, and a clinical prediction model was created. This study involved 573 patients who underwent coronary angiography at our hospital because of chest pain from January 2020 to April 2022. They were divided into CSF group (249 cases) and noncoronary slow flow (NCF) group (324 cases) according to the coronary blood flow results. According to a 7:3 ratio, the patients were categorized into a training group consisting of 402 cases and a validation group consisting of 171 cases. The outcome was assessed by employing multiple logistic regression analysis to examine the factors that influenced it. The model's recognizability was assessed by calculating the consistency index and plotting the receiver operating characteristic curve. Its consistency was assessed by calibration curve, decision curve, and Hosmer-Lemeshow testing goodness-of-fit. The multivariate model included factors such as male, BMI, smoking, diabetes, ursolic acid, and high-density lipoprotein cholesterol. The model validation showed that the consistency index was 0.714, and the external validation set had a consistency index of 0.741. The areas under the curve for the training and external validation sets were respectively 0.730 (95% CI: 0.681-0.779) and 0.770 (95%CI: 0.699-0.841). Nomogram calibration curves indicated intense calibration, and the results of the Hosmer-Lemeshow goodness-of-fit test indicated that χ² = 1.118, P = .572. The nomogram combining various risk factors can be used for individualized predictions of CSF patients and then facilitate prompt and specific treatment.

Development and Validation of Machine Learning Models for Identifying Prediabetes and Diabetes in Normoglycemia.

Prediabetes and diabetes are both abnormal states of glucose metabolism (AGM) that can lead to severe complications. Early detection of AGM is crucial for timely intervention and treatment. However, fasting blood glucose (FBG) as a mass population screening method may fail to identify some individuals who are actually AGM but with normoglycemia. This study aimed to develop and validate machine learning (ML) models to identify AGM among individuals with normoglycemia using routine health check-up indicators. According to the American Diabetes Association (ADA) criteria, participants with normoglycemia (FBG≤5.6mmol/L) were collected from 2019 to 2023, and then divided into AGM and Normalgroups using glycosylated haemoglobin (HbA1c) 5.7% as the threshold. Data from 2019 to 2022 were divided into training and internal validation sets at a 7:3 ratio, while data from 2023 were used as the external validation set. Seven ML algorithms-including logistic regression (LR), random forest (RF), support vector machine (SVM), extreme gradient boosting machine, multilayer perceptron (MLP), light gradient boosting machine (LightGBM), and categorical boosting (CatBoost)-were used to build models for identifying AGM in normoglycemia population. Model performance was evaluated using the area under the receiver operating characteristic curve (auROC) and the precision-recall curve (auPR). The feature contributions to the optimal model was visualised using the SHapley Additive exPlanations (SHAP). Finally, an intuitive and user-friendly interactive interface was developed. A total of 59,259 participants were finally enroled in this study, and then divided into the training set of 32,810, the internal validation set of 14,060, and the external validation set of 12,389. The Catboost model outperformed the others with auROC of 0.806 and 0.794 for the internal and external validation set, respectively. Age was the most important feature influencing the performance of the CatBoost model, followed by fasting blood glucose, red blood cells, haemoglobin, body mass index, and triglyceride-glucose. A well-performed ML model to identify AGM in the normoglycemia population was built, offering significant potential for early intervention and treatment of AGM that would otherwise have been missed.

A Stacked Multimodality Model Based on Functional MRI Features and Deep Learning Radiomics for Predicting the Early Response to Radiotherapy in Nasopharyngeal Carcinoma

BackgroundThis study aimed to construct and assess a comprehensive model that integrates MRI-derived deep learning radiomics, functional imaging (fMRI), and clinical indicators to predict early efficacy of radiotherapy in nasopharyngeal carcinoma (NPC). MethodsThis retrospective study recruited NPC patients with radiotherapy from two Chinese hospitals between October 2018 and July 2022, divided into a training set (hospital I, 194 cases), an internal validation set (hospital I, 82 cases), and an external validation set (hospital II, 40 cases). We extracted 3404 radiomic features and 2048 deep learning characteristics from MRI modalities - T1WI, CE-T1WI, T2WI, and T2WI/FS. Additionally, both the ADC and its maximum (ADCmax) from DWI imaging, along with TBF and its maximum (TBFmax) from ASL imaging were derived. We used four classifiers (LR, XGBoost, SVM and KNN) and stacked algorithm as model construction methods. The receiver operating characteristic (ROC) curve (AUC) and decision curve analysis (DCA) was used to assess models. ResultsThe manual radiomics model leveraging XGBoost and the deep learning model based on KNN (the AUCs in the training set: 0.909, 0.823, respectively) showed better predictive efficacy than other machine learning algorithms. The stacked model that integrated MRI-based deep learning radiomics, fMRI, and hematological indicators, has a large improvement of AUC in the training set [0.984 (95%CI: 0.972 - 0.996)], the internal validation set [0.936 (95%CI: 0.885 - 0.987)], and the external validation set [0.959 (95%CI: 0.901-1)]. ConclusionsOur research has developed a clinical-radiomics integrated model based on MRI which can predict early radiotherapy response in NPC and provide guidance for personalized treatment.

Intratumoral and peritumoral radiomics of MRIs predicts pathologic complete response to neoadjuvant chemoimmunotherapy in patients with head and neck squamous cell carcinoma

BackgroundFor patients with locally advanced head and neck squamous cell carcinoma (HNSCC), combined programmed death receptor-1 inhibitor and chemotherapy improved response rate to neoadjuvant therapy. However, treatment response varies among...

Development of a risk score for predicting one-year mortality in patients with atrial fibrillation using XGBoost-assisted feature selection.

There are no tools specifically designed to assess mortality risk in patients with atrial fibrillation (AF). This study aimed to utilize machine learning methods to identify pertinent variables and develop an easily applicable prognostic score to predict 1-year mortality in AF patients. This study, based on the Medical Information Mart for Intensive Care-IV (MIMIC-IV) database, focused on patients aged 18 years and older with AF. A critical care database from China was the external validation set. The importance of variables from XGBoost guided the development of a logistic model, forming the basis for an AF scoring model. Records of of 26 365 AF patients were obtained from the MIMIC-IV database. The external validation dataset included 231 AF patients. The CRAMB score (Charlson comorbidity index, readmission, age, metastatic solid tumor, and maximum blood urea nitrogen concentration) outperformed the CCI and CHA2DS2-VASc scores, demonstrating superior predictive value for 1-year mortality. In the test set, the area under the receiver operating characteristic (AUC) for the CRAMB score was 0.765 (95% confidence interval [CI], 0.753-0.776), while in the external validation set, it was 0.582 (95% CI, 0.502-0.657). The simplicity of the CRAMB score makes it user-friendly, allowing for coverage of a broader and more heterogeneous AF population.

Applying Deep-Learning Algorithm Interpreting Kidney, Ureter, and Bladder (KUB) X-Rays to Detect Colon Cancer.

Early screening is crucial in reducing the mortality of colorectal cancer (CRC). Current screening methods, including fecal occult blood tests (FOBT) and colonoscopy, are primarily limited by low patient compliance and the invasive nature of the procedures. Several advanced imaging techniques such as computed tomography (CT) and histological imaging have been integrated with artificial intelligence (AI) to enhance the detection of CRC. There are still limitations because of the challenges associated with image acquisition and the cost. Kidney, ureter, and bladder (KUB) radiograph which is inexpensive and widely used for abdominal assessments in emergency settings and shows potential for detecting CRC when enhanced using advanced techniques. This study aimed to develop a deep learning model (DLM) to detect CRC using KUB radiographs. This retrospective study was conducted using data from the Tri-Service General Hospital (TSGH) between January 2011 and December 2020, including patients with at least one KUB radiograph. Patients were divided into development (n = 28,055), tuning (n = 11,234), and internal validation (n = 16,875) sets. An additional 15,876 patients were collected from a community hospital as the external validation set. A 121-layer DenseNet convolutional network was trained to classify KUB images for CRC detection. The model performance was evaluated using receiver operating characteristic curves, with sensitivity, specificity, and area under the curve (AUC) as metrics. The AUC, sensitivity, and specificity of the DLM in the internal and external validation sets achieved 0.738, 61.3%, and 74.4%, as well as 0.656, 47.7%, and 72.9%, respectively. The model performed better for high-grade CRC, with AUCs of 0.744 and 0.674 in the internal and external sets, respectively. Stratified analysis showed superior performance in females aged 55-64 with high-grade cancers. AI-positive predictions were associated with a higher long-term risk of all-cause mortality in both validation cohorts. AI-enhanced KUB X-ray analysis can enhance CRC screening coverage and effectiveness, providing a cost-effective alternative to traditional methods. Further prospective studies are necessary to validate these findings and fully integrate this technology into clinical practice.

Decoding marker genes and immune landscape of unstable carotid plaques from cellular senescence

Recently, cellular senescence-induced unstable carotid plaques have gained increasing attention. In this study, we utilized bioinformatics and machine learning methods to investigate the correlation between cellular senescence and the pathological mechanisms of unstable carotid plaques. Our aim was to elucidate the causes of unstable carotid plaque progression and identify new therapeutic strategies. First, differential expression analysis was performed on the test set GSE43292 to identify differentially expressed genes (DEGs) between the unstable plaque group and the control group. These DEGs were intersected with cellular senescence-associated genes to obtain 40 cellular senescence-associated DEGs. Subsequently, key genes were then identified through weighted gene co-expression network analysis, random forest, Recursive Feature Elimination for Support Vector Machines algorithm and cytoHubba plugin. The intersection yielded 3 CSA-signature genes, which were validated in the external validation set GSE163154. Additionally, we assessed the relationship between these CSA-signature genes and the immune landscape of the unstable plaque group. This study suggests that cellular senescence may play an important role in the progression mechanism of unstable plaques and is closely related to the influence of the immune microenvironment. Our research lays the foundation for studying the progression mechanism of unstable carotid plaques and provides some reference for targeted therapy.

Development and internal and external validation of a nomogram model for predicting the risk of chronic kidney disease progression in IgA nephropathy patients.

IgA nephropathy (IgAN) is the most common primary glomerular disease in chronic kidney disease (CKD), exhibiting significant heterogeneity in both clinical and pathological presentations. We aimed to explore the risk factors influencing short-term prognosis (≥90 days) and to construct a nomogram model for evaluating the risk of CKD progression in IgAN patients. Clinical and pathological data of patients diagnosed with IgAN through biopsy at two centers were retrospectively collected. Logistic regression was employed to analyze the training cohort dataset and identify the independent predictors to construct a nomogram model based on the final variables. The predictive model was validated both internally and externally, with its performance assessed using the area under the curve (AUC), calibration curves, and decision curve analysis. Out of the patients in the modeling group, 129 individuals (41.6%) did not achieve remission following 3 months of treatment, indicating a high risk of CKD progression. A multivariate logistic regression analysis demonstrated that body mass index, urinary protein excretion, and tubular atrophy/interstitial fibrosis were identified as independent predictors for risk stratification. A nomogram model was formulated utilizing the final variables. The AUCs for the training set, internal validation set, and external validation set were 0.746 (95% confidence intervals (CI) [0.691-0.8]), 0.764 (95% CI [0.68-0.85]), and 0.749 (95% CI [0.65-0.85]), respectively. The validation of the subgroup analysis also demonstrated a satisfactory AUC. This study developed and validated a practical nomogram that can individually predict short-term treatment outcomes (≥90 days) and the risk of CKD progression in IgAN patients. It provides reliable guidance for timely and personalized intervention and treatment strategies.

Integrating (deep) machine learning and cheminformatics for predicting human intestinal absorption of small molecules

The oral route is the most preferred route for drug delivery, due to which the largest share of the pharmaceutical market is represented by oral drugs. Human intestinal absorption (HIA) is closely related to oral bioavailability making it an important factor in predicting drug absorption. In this study, we focus on predicting drug permeability at HIA as a marker for oral bioavailability. A set of 2648 compounds were collected from some early as well as recent works and curated to build a robust dataset. Five machine learning (ML) algorithms have been trained with a set of molecular descriptors of these compounds which have been selected after rigorous feature engineering. Additionally, two deep learning models - graph convolution neural network (GCNN) and graph attention network (GAT) based model were developed using the same set of compounds to exploit the predictability with automated extracted features. The numerical analyses show that out the five ML models, Random forest and LightGBM could predict with an accuracy of 87.71 % and 86.04 % on the test set and 81.43 % and 77.30 % with the external validation set respectively. Whereas with the GCNN and GAT based models, the final accuracy achieved was 77.69 % and 78.58 % on test set and 79.29 % and 79.42 % on the external validation set respectively. We believe deployment of these models for screening oral drugs can provide promising results and therefore deposited the dataset and models on the GitHub platform (https://github.com/hridoy69/HIA).

Diagnostic precision in thyroid-associated ophthalmopathy using multi-center radiomics with 99mTc-DTPA SPECT/CT

To explore the performance of 99mTc-diethylene triaminepentaacetic acid (DTPA) SPECT/CT texture analysis in evaluating the activity of thyroid-associated ophthalmopathy (TAO) . This retrospective study examined 115 TAO patients from a single institution as an internal cohort and 58 TAO patients from another institution as an external validation set. Patients in the internal cohort were randomly divided into training (n = 81) and internal validation sets (n = 34). Radiomics signatures were constructed with the minimal redundancy maximal relevance and least absolute shrinkage and selection operator algorithms in training set. Multivariate logistic regression analysis was used to develop a clinical model and a combined clinical–radiomics model. Diagnostic performance of models was evaluated using receiver operating characteristic curve analysis, calibration curves and decision curve analysis. Compared with CT and SPECT radiomics models, Rad-scoreSPECT/CT demonstrated the best performance with areas under the receiver operating characteristic curve of 0.94 and 0.91 in the training and test sets, respectively. The combined clinical-radiomics model exhibited significantly better performance in evaluating TAO activity. Our results demonstrate the validity of a multimodal radiomic model of 99mTc-DTPA-SPECT/CT to assess TAO activity. The combined clinical-radiomics model exhibited significantly better diagnostic performance than the clinical model.

AngioPy: an open-source, deep learning-driven tool for coronary artery segmentation

Abstract Background Quantitative coronary angiography (QCA) permits the objective assessment of coronary artery disease. However, traditional edge detection algorithms often struggle with accurate vessel segmentation due to the complexity and variable quality of angiographic images. As a result, manual correction is frequently needed, which is a major limitation of current QCA systems. Purpose We developed angioPy, a deep learning-driven tool for vessel segmentation that employs user-defined ground truth points to minimise manual correction. We compared its performance without correction with an established QCA system. Methods angioPy was developed using 2455 images from the Fractional Flow Reserve versus Angiography for Multivessel Evaluation 2 (FAME 2) study. Deep learning models were constructed using the U-Net architecture with one of three popular backbones for image classification: ResNet101, DenseNet121, and InceptionResNet-v2. Critically, the model was constructed to integrate the user’s clinical expertise through the selection of a 5-10 ground-truth points along the length of the vessel of interest including the desired start and end point of vessel segmentation. These ground truth points were added to a separate channel of the input image. Five-fold cross validation was performed using proportions of 3:1:1 for training, validation, and test sets, respectively. External validation was performed on a separate dataset of 580 images not used for model development. For both datasets, ground truth segmentation masks were provided by interventional cardiologists using specialised in-house software. A separate analysis was performed in a cohort of 74 patients with mild/moderate stenoses that underwent vessel segmentation using both angioPy and an established commercial QCA package (Medis QFR®). Vessel dimensions at stenoses (proximal and distal reference, minimal luminal diameter) were extracted from both segmentation approaches and compared (609 diameters in total). Results The best performing model performed segmentation with an average F1 score of 0.927 (pixel accuracy 0.998, precision 0.925, sensitivity 0.930, specificity 0.999) with 99.2% of masks exhibiting an F1 score &amp;gt; 0.8 (Figure 1). Simliar results were achieved in the external validation set (F1 score 0.924, pixel accuracy 0.997, precision 0.921, sensitivity 0.929, specificity 0.999). Stenosis dimensions measured with angioPy (mean diameter 3.54 ±1.15 mm) exhibited excellent agreement with QCA (r=0.95 [95% CI 0.95-0.96], p&amp;lt;0.001; mean difference -0.18 mm [limits of agreement: -0.84 to 0.49]) (Figure 2). Minimal luminal diameter (mean 2.93 ±0.91 mm) also exhibited strong agreement (r=0.93 [95% CI 0.91-0.95], p&amp;lt;0.001; mean difference -0.06 mm [limits of agreement: -0.70 to 0.59]. Conclusion angioPy performs rapid and accurate coronary segmentation without the need for manual correction. Available as an open-source tool, angioPy has the potential to increase the efficiency and reliability of QCA.Figure 1.angioPy segmentationFigure 2.angioPy vs QCA (Medis)