Logistic Regression Classifier Research Articles

Research and implementation of the medical text analysis algorithm for predicting mortality

Mortality prediction has a role to play in the development of a descriptive measure of the quality of care that provides a fair and equitable means of comparing and evaluating hospitals. This article describes a study of a medical text analysis algorithm for mortality prediction that used big data in the form of unstructured medical notes. The article describes the concept of using text mining technology for medical systems, a method for preprocessing medical data to predict patient mortality, an algorithm for predicting patient deaths based on the logistic regression classifier and presents a software module for implementing the proposed algorithm.

Hybrid optimal feature selection approach for internet of things based medical data analysis for prognosis

<p>Healthcare is very important application domain in internet of things (IoT). The aim is to provide a novel combined feature selection (FS) methods like univariate (UV) with tree-based methods (TB), recursive feature elimination (RFE) with least absolute shrinkage selection operator (LASSO), mutual information (MI) with genetic algorithm (GA) and embedded methods (EM) with univariate has been applied to internet of medical things (IoMT)based heart disease dataset. The well-suited machine learning algorithms for IoT medical data are logistic regression (LR) and support vector machine (SVM). Each combined method has been applied to the machine learning algorithms to find the best classifier for prognosis. The various performance metrices has been calculated for all the combined feature selection methods for logistic regression and support vector machine and found that for precise classification could be done using recursive elimination feature selection method with LASSO applied to logistic regression achieved a better performance than all other combined methods with high accuracy, sensitivity and high area under curve. Decision has been taken by data analytics that RFE+LASSO using LR feature selection method will provide an overall better performance for IoT based medical heart disease dataset after comparing all other combined methods with LR and SVM classifiers<em>. </em></p>

The diagnostic value of multimodal imaging based on MR combined with ultrasound in benign and malignant breast diseases

We aimed to construct and validate a multimodality MRI combined with ultrasound based on radiomics for the evaluation of benign and malignant breast diseases. The preoperative enhanced MRI and ultrasound images of 131 patients with breast diseases confirmed by pathology in Aerospace Center Hospital from January 2021 to August 2023 were retrospectively analyzed, including 73 benign diseases and 58 malignant diseases. Ultrasound and 3.0 T multiparameter MRI scans were performed in all patients. Then, all the data were divided into training set and validation set in a 7:3 ratio. Regions of interest were drawn layer by layer based on ultrasound and MR enhanced sequences to extract radiomics features. The optimal radiomic features were selected by the best feature screening method. Logistic Regression classifier was used to establish models according to the best features, including ultrasound model, MRI model, ultrasound combined with MRI model. The model efficacy was evaluated by the area under the curve (AUC) of the receiver operating characteristic, sensitivity, specificity, and accuracy. The F-test based on ANOVA was used to screen out 20 best ultrasonic features, 11 best MR Features, and 14 best features from the combined model. Among them, texture features accounted for the largest proportion, accounting for 79%.The ultrasound combined with MR Image fusion model based on logistic regression classifier had the best diagnostic performance. The AUC of the training group and the validation group were 0.92 and 091, the sensitivity was 0.80 and 0.67, the specificity was 0.90 and 0.94, and the accuracy was 0.84 and 0.79, respectively. It was better than the simple ultrasound model (AUC of validation set was 0.82) or the simple MR model (AUC of validation set was 0.85). Compared with the traditional ultrasound or magnetic resonance diagnosis of breast diseases, the multimodal model of MRI combined with ultrasound based on radiomics can more accurately predict the benign and malignant breast diseases, thus providing a better basis for clinical diagnosis and treatment.

Pseudo-resting-state functional MRI derived from dynamic susceptibility contrast perfusion MRI can predict cognitive impairment in glioma.

Resting-state functional MRI (rs-fMRI) can be used to estimate functional connectivity (FC) between different brain regions, which may be of value for identifying cognitive impairment in patients with brain tumors. Unfortunately, neither rs-fMRI nor neurocognitive assessments are routinely assessed clinically, mostly due to limitations in exam time and cost. Since DSC perfusion MRI is often used clinically to assess tumor vascularity and similarly uses a gradient echo-EPI sequence for T2*sensitivity, we theorized a "pseudo-rs-fMRI" signal could be derived from DSC perfusion to simultaneously quantify FC and perfusion metrics, and these metrics can be used to estimate cognitive impairment in patients with brain tumors. N=24 consecutive patients with gliomas were enrolled in a prospective study that included DSC perfusion MRI, rs-fMRI, and neurocognitive assessment. Voxel-wise modeling of contrast bolus dynamics during DSC acquisition was performed and then subtracted from the original signal to generate a residual "pseudo-rs-fMRI" signal. Following the pre-processing of pseudo-rs-fMRI, full rs-fMRI, and a truncated version of the full rs-fMRI (first 100 timepoints) data, the default mode, motor, and language network maps were generated with atlas-based ROIs. Dice scores were calculated for the resting-state network maps from pseudo-rs-fMRI and truncated rs-fMRI using the full rs-fMRI maps as reference. Seed-to-voxel and ROI-to-ROI analyses were performed to assess FC differences between cognitively impaired and non-impaired patients. Dice scores for the group-level and patient-level (mean±SD) default mode, motor, and language network maps using pseudo-rs-fMRI were 0.905/0.689±0.118 (group/patient), 0.973/0.730±0.124, and 0.935/0.665±0.142, respectively. There was no significant difference in Dice scores between pseudo-rs-fMRI and the truncated rs-fMRI default mode (P=0.97) or language networks (P=0.30), but there was a difference in motor networks (P=0.02). A multiple logistic regression classifier applied to ROI-to-ROI FC networks using pseudo-rs-fMRI could identify cognitively impaired patients (Sensitivity=84.6%, Specificity=63.6%, ROC AUC=0.7762±0.0954 (SE), P=0.0221) and performance was not significantly different than full rs-fMRI predictions (AUC=0.8881±0.0733 (SE), P=0.0013, P=0.29 compared to pseudo-rs-fMRI). DSC perfusion MRI-derived pseudo-rs-fMRI data can be used to perform typical rs-fMRI FC analyses that may identify cognitive decline in patients with brain tumors while still simultaneously performing perfusion analyses.ABBREVIATIONS: AUC = Area under curve; BOLD = Blood oxygenation level dependent; FC = Functional connectivity; MNI = Montreal Neurological Institute; ROC = Receiver operating characteristic; Rs-fMRI = Resting-state functional MRI.

An Electronic Health Record Model for Predicting Risk of Hepatic Fibrosis in Primary Care Patients.

One challenge for primary care providers caring for patients with nonalcoholic fatty liver disease is to identify those at the highest risk for clinically significant liver disease. To derive a risk stratification tool using variables from structured electronic health record (EHR) data for use in populations which are disproportionately affected with obesity and diabetes. We used data from 344 participants who underwent Fibroscan examination to measure liver fat and liver stiffness measurement [LSM]. Using two approaches, multivariable logistic regression and random forest classification, we assessed risk factors for any hepatic fibrosis (LSM > 7kPa) and significant hepatic fibrosis (> 8kPa). Possible predictors included data from the EHR for age, gender, diabetes, hypertension, FIB-4, body mass index (BMI), LDL, HDL, and triglycerides. Of 344 patients (56.4% women), 34 had any hepatic fibrosis, and 15 significant hepatic fibrosis. Three variables (BMI, FIB-4, diabetes) were identified from both approaches. When we used variable cut-offs defined by Youden's index, the final model predicting any hepatic fibrosis had an AUC of 0.75 (95% CI 0.67-0.84), NPV of 91.5% and PPV of 40.0%. The final model with variable categories based on standard clinical thresholds (i.e., BMI ≥ 30kg/m2; FIB-4 ≥ 1.45) had lower discriminatory ability (AUC 0.65), but higher PPV (50.0%) and similar NPV (91.3%). We observed similar findings for predicting significant hepatic fibrosis. Our results demonstrate that standard thresholds for clinical risk factors/biomarkers may need to be modified for greater discriminatory ability among populations with high prevalence of obesity and diabetes.

Abstract PO5-13-06: Classifying HER2-low breast cancer using a combination of ERBB2 mRNA expression and altered genes

Abstract Background It has been recently demonstrated that some HER2-low, defined as immunohistochemistry (IHC) 1+ or 2+ with no gene amplification by FISH, breast cancer (BC) patients respond to trastuzumab deruxtecan (T-DXd). Results of the DAISY trial also suggested clinical activity with T-DXd in some of those classified as HER2-0 cancers by IHC, indicating an unmet need to better identify cancers that may truly respond to T-DXd. We compared ERBB2 (HER2) mRNA expression obtained from whole-transcriptome sequencing with IHC/FISH assignment of HER2 status. Furthermore, we constructed a classifier using ERBB2 expression and alterations in other genes as a proof of concept to illustrate classification of BC samples into HER2-0 versus HER2-low status. Methods We chose consecutive HR positive/HER2-negative BC samples that were submitted for OncoExTraTM testing between April 2020 and October 2022. The OncoExTra test uses tumor-normal whole exome and whole transcriptome sequencing to detect somatic single base substitutions, indels, copy number alterations, gene fusions and alternative transcripts. In addition, we investigated the expression profile of select genes for this analysis. We utilized OncoExTra data to examine the relationship between HER2 IHC status and gene expression, mutation and copy number profiles of selected genes, and built a classifier to predict HER2 status. Results A total of 279 BC samples were analyzed, including 106 HER2-IHC 0, 120 HER2-IHC 1+ and 53 HER2-IHC 2+. Of these, 273 were primary and 6 were metastatic samples. The distributions of patient age and tumor fraction were similar among these categories (p=0.54 and p=0.41, respectively; one-way ANOVA). ERBB2 expression differed among all three HER2-IHC categories and was lowest in HER2-0 and highest in HER2-2+ (HER2-0 vs HER2-1+, p< 0.001; HER2-0 vs HER2-2+, p< 0.0001; HER2-1+ vs HER2-2+, p=0.011; HER2-0 vs HER2-low, p< 0.0001; Mann-Whitney U test in all comparisons). Five genes were mutated in more than 10% of samples: PIK3CA (45.5%), GATA3 (15.4%), CDH1 (12.5%), MAP3K1 (11.1%) and TP53 (10.8%). Mutations in two genes, GATA3 and PTEN, appeared to differ in frequency between the HER2-0 and HER2-low categories (Table 1). We selected 4 genes with mutations, 2 genes with copy number changes, and expression from ERBB2, ESR1, CD274, HLA-A, HLA-B and HLA-C to train a logistic regression classifier to predict HER2 IHC status. The classifier was trained on 163 samples, hyperparameter tuning was done using 55 samples, and testing was performed on 61 samples. Preliminary results indicated that of the 28 HER2-IHC 0 samples in the test set, 17 (65%) were classified as HER2-low. Further development and evaluation of the classifier using a blinded testing set is currently in progress. Conclusion In this cohort of BC samples, ERBB2 mRNA expression was positively associated with HER2 protein IHC status. Additional studies are required to determine whether a classifier including ERBB2 mRNA expression could be used to identify patients for T-DXd therapy. The relative enrichment of PTEN alterations in HER2-IHC 0 samples suggests that mTOR/AKT inhibitors may sometimes be appropriate in patients who are not eligible for T-DXd therapy, and further investigation should be considered. Table 1. Number (frequency) of altered genes by HER2 IHC status. Citation Format: Gargi Basu, Niru Chennagiri, Turgut Dogruluk, David Hall, Jess Hoag, Cynthia Flannery, Snehal Thakkar, Melanie Palomares, Frederick Baehner, Lajos Pusztai. Classifying HER2-low breast cancer using a combination of ERBB2 mRNA expression and altered genes [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-13-06.

Development and validation of a deep learning radiomics model with clinical-radiological characteristics for the identification of occult peritoneal metastases in patients with pancreatic ductal adenocarcinoma.

Occult peritoneal metastases (OPM) in patients with pancreatic ductal adenocarcinoma (PDAC) are frequently overlooked during imaging. The authors aimed to develop and validate a computed tomography (CT)-based deep learning-based radiomics (DLR) model to identify OPM in PDAC before treatment. This retrospective, bicentric study included 302 patients with PDAC (training: n =167, OPM-positive, n =22; internal test: n =72, OPM-positive, n =9: external test, n =63, OPM-positive, n =9) who had undergone baseline CT examinations between January 2012 and October 2022. Handcrafted radiomics (HCR) and DLR features of the tumor and HCR features of peritoneum were extracted from CT images. Mutual information and least absolute shrinkage and selection operator algorithms were used for feature selection. A combined model, which incorporated the selected clinical-radiological, HCR, and DLR features, was developed using a logistic regression classifier using data from the training cohort and validated in the test cohorts. Three clinical-radiological characteristics (carcinoembryonic antigen 19-9 and CT-based T and N stages), nine HCR features of the tumor, 14 DLR features of the tumor, and three HCR features of the peritoneum were retained after feature selection. The combined model yielded satisfactory predictive performance, with an area under the curve (AUC) of 0.853 (95% CI: 0.790-0.903), 0.845 (95% CI: 0.740-0.919), and 0.852 (95% CI: 0.740-0.929) in the training, internal test, and external test cohorts, respectively (all P <0.05). The combined model showed better discrimination than the clinical-radiological model in the training (AUC=0.853 vs. 0.612, P <0.001) and the total test (AUC=0.842 vs. 0.638, P <0.05) cohorts. The decision curves revealed that the combined model had greater clinical applicability than the clinical-radiological model. The model combining CT-based DLR and clinical-radiological features showed satisfactory performance for predicting OPM in patients with PDAC.

Preoperative Risk Stratification for Gastric Cancer: The Establishment of Dual-Energy CT-Based Radiomics Using Prospective Datasets at Two Centers

ObjectiveTo evaluate the performance of dual-energy CT (DECT)-based radiomics models for identifying high-risk histopathologic phenotypes - serosal invasion (pT4a), lymph node metastasis (LNM), lymphovascular invasion (LVI) and perineural invasion (PNI) in gastric cancer. Material and MethodsThis prospective bi-center study recruited histologically confirmed gastric adenocarcinoma patients who underwent triple-phase enhanced DECT before gastrectomy between January 2021 and July 2023. Radiomics features were extracted from polychromatic/monochromatic (40keV, 100 keV)/iodine images at arterial/venous/delay phase, respectively. Predictive features were selected in the training dataset using logistic regression classifier, and trained models were applied to the external validation dataset. Performances of clinical models, conventional contrast enhanced CT (CECT) models and DECT models were evaluated using areas under the receiver operating characteristic curve (AUCs). ResultsIn total, 503 patients were recruited: 396 at training dataset (60.1 ± 10.8 years, 110 females, 286 males) and 107 at validation dataset (61.4 ± 9.5 years, 29 females, 78 males). DECT models dichotomizing pT4a, LNM, LVI, and PNI achieved AUCs of 0.891, 0.817, 0.834, and 0.889, respectively, in the validation dataset, similar with the CECT models. In the training dataset, compared with the CECT model, the DECT model provided increased performance for identifying pT4a, LNM, LVI (all P＜0.05), and similar performance for stratifying PNI (P = 0.104). The DECT models was associated with patient disease-free survival (all P ＜0.05). ConclusionDECT radiomics can stratify patients preoperatively according to high-risk histopathologic phenotypes for gastric cancer and are associated with patient disease-free survival in the training dataset.

A retrospective study of congenital anomalies and associated risk factors among children admitted at a tertiary hospital in northwestern Tanzania.

Congenital anomalies in Sub-Sahara Africa (SSA) are understudied despite the significant pediatric health burden. This retrospective longitudinal hospital-based study evaluated the records of 326 inpatient children under the age of two years with congenital anomalies at Bugando Medical Centre, a tertiary referral hospital in northwestern Tanzania. Classical logistic regression was used in the analysis of congenital malformation of muscles, gastrointestinal malformation, oral facial clefts, neural tube defects, and skeletal malformations. A modified poisson regression was used to model risk factors for Central Nervous System (CNS) hydrocephalus and congenital heart disease (CHD). A majority (78.8%) of children included in the study were less than six months of age. Nearly half (48.8%) were diagnosed with CHD followed by CNS hydrocephalus (10.4%) and congenital malformation of muscles (8.9%). Babies whose mothers missed periconceptual folic acid supplementation had 83% higher risk of hydrocephalus (aPR = 1.83, 95% CI = 1.11-1.96) and 78% higher for CHD (aPR = 1.78, 95% CI = 1.31-1.94). Male children had 1.67 higher odds of muscular congenital malformations (aOR = 1.67, 95% CI = 1.23-1.89). Less than 37 gestational age had a 1.86 higher odds of muscular congenital malformations (aOR = 1.86, 95% CI = 1.53-3.66). Our study highlights the critical need for folic acid supplementation and establishes a need for a registry and the potential for mapping.

Identification of patients with internet gaming disorder via a radiomics-based machine learning model of subcortical structures in high-resolution T1-weighted MRI

It is of vital importance to establish an objective and reliable model to facilitate the early diagnosis and intervention of internet gaming disorder (IGD). A total of 133 patients with IGD and 110 healthy controls (HCs) were included. We extracted radiomic features of subcortical structures in high-resolution T1-weighted MRI. Different combinations of four feature selection methods (analysis of variance, Kruskal–Wallis, recursive feature elimination and relief) and ten classification algorithms were used to identify the most robust combined models for distinguishing IGD patients from HCs. Furthermore, a nomogram incorporating radiomic signatures and independent clinical factors was developed. Calibration curve and decision curve analyses were used to evaluate the nomogram. The combination of analysis of variance selector and logistic regression classifier identified that the radiomic model constructed with 20 features from the right caudate nucleus and amygdala showed better IGD screening performance. The radiomic model produced good areas under the curves (AUCs) in the training, validation and test cohorts (AUCs of 0.961, 0.903 and 0.895, respectively). In addition, sex, internet addiction test scores and radiomic scores were included in the nomogram as independent risk factors for IGD. Analysis of the correction curve and decision curve showed that the clinical-radiomic model has good reliability (C-index: 0.987). The nomogram incorporating radiomic features of subcortical structures and clinical characteristics achieved satisfactory classification performance and could serve as an effective tool for distinguishing IGD patients from HCs.

Machine learning prediction of one-year mortality after percutaneous coronary intervention in acute coronary syndrome patients

BackgroundMachine learning (ML) models have the potential to accurately predict outcomes and offer novel insights into inter-variable correlations. In this study, we aimed to design ML models for the prediction of 1-year mortality after percutaneous coronary intervention (PCI) in patients with acute coronary syndrome. MethodsThis study was performed on 13,682 patients at Tehran Heart Center from 2015 to 2021. Patients were split into 70:30 for testing and training. Four ML models were designed: a traditional Logistic Regression (LR) model, Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Ada Boost models. The importance of features was calculated using the RF feature selector and SHAP based on the XGBoost model. The Area Under the Receiver Operating Characteristic Curve (AUC-ROC) for the prediction on the testing dataset was the main measure of the model's performance. ResultsFrom a total of 9073 patients with >1-year follow-up, 340 participants died. Higher age and higher rates of comorbidities were observed in these patients. Body mass index and lipid profile demonstrated a U-shaped correlation with the outcome. Among the models, RF had the best discrimination (AUC 0.866), while the highest sensitivity (80.9%) and specificity (88.3%) were for LR and XGBoost models, respectively. All models had AUCs of >0.8. ConclusionML models can predict 1-year mortality after PCI with high performance. A classic LR statistical approach showed comparable results with other ML models. The individual-level assessment of inter-variable correlations provided new insights into the non-linear contribution of risk factors to post-PCI mortality.

Multiparametric MRI-based radiomic nomogram for predicting HER-2 2+ status of breast cancer

ObjectiveTo explore the application of multiparametric MRI-based radiomic nomogram for assessing HER-2 2+ status of breast cancer (BC) MethodsPatients with pathology-proven HER-2 2+ invasive BC, who underwent preoperative MRI were divided into training (72 patients, 21 HER-2-positive and 51 HER-2-negative) and validation (32 patients, 9 HER-2-positive and 23 HER-2-negative) sets by randomization. All were classified as HER-2 2+ FISH-positive (HER-2-positive) or -negative (HER-2-negative) according to IHC and FISH. The 3D VOI was drawn on MR images by two radiologists. ADC, T2WI, and DCE images were analyzed separately to extract features (n = 1906). L1 regularization, F-test, and other methods were used to reduce dimensionality. Binary radiomics prediction models using features from single or combined imaging sequences were constructed using logistic regression (LR) classifier then and validated on a validation dataset. To build a radiomics nomogram, multivariate LR analysis was conducted to identify independent indicators. An evaluation of the model's predictive efficacy was made using AUC. ResultsOn the basis of combined ADC, T2WI, and DCE images, ten radiomic features were extracted following feature dimensionality reduction. There was superior diagnostic efficiency of radiomic signature using all three sequences compared to either one or two sequences (AUC for training group: 0.883; AUC for validation group: 0.816). Based on multivariate LR analysis, radiomic signature and peritumoral edema were independent predictors for identifying HER-2 2 +. In both training and validation datasets, nomograms combining peritumoral edema and radiomics signature demonstrated an effective discrimination (AUCs were respectively 0.966 and 0. 884). ConclusionThe nomogram that incorporated peritumoral edema and multiparametric MRI-based radiomic signature can be used to effectively predict the HER-2 2+ status of BC.

CYBER BULLYING DETECTION: AN ENSEMBLE BASED MACHINE LEARNING APPROACH

Research on cyberbullying detection.To identify control and reduce the bullying contents spread over social media sites. Though data collection and feature engineering process has been elaborated, yet most of the emphasis is on feature selection algorithms. Thus there is an extensive need to identify, control and reduce the bullying contents spread over social media sites, which has motivated us to conduct this research to automate the detection process of offensive language or cyberbullying. In our work, Logistic Regression and Bagging ensemble model classifier have performed individually best in detecting cyberbullying which has been outperformed by our proposed SLE and DLE voting classifiers. Our proposed SLE and DLE models yield the best performance of 96% when TF-IDF (Unigram) feature extraction is applied with K-Fold cross-validation.

Identification of predictive patient characteristics for assessing the probability of COVID-19 in-hospital mortality.

As the world emerges from the COVID-19 pandemic, there is an urgent need to understand patient factors that may be used to predict the occurrence of severe cases and patient mortality. Approximately 20% of SARS-CoV-2 infections lead to acute respiratory distress syndrome caused by the harmful actions of inflammatory mediators. Patients with severe COVID-19 are often afflicted with neurologic symptoms, and individuals with pre-existing neurodegenerative disease have an increased risk of severe COVID-19. Although collectively, these observations point to a bidirectional relationship between severe COVID-19 and neurologic disorders, little is known about the underlying mechanisms. Here, we analyzed the electronic health records of 471 patients with severe COVID-19 to identify clinical characteristics most predictive of mortality. Feature discovery was conducted by training a regularized logistic regression classifier that serves as a machine-learning model with an embedded feature selection capability. SHAP analysis using the trained classifier revealed that a small ensemble of readily observable clinical features, including characteristics associated with cognitive impairment, could predict in-hospital mortality with an accuracy greater than 0.85 (expressed as the area under the ROC curve of the classifier). These findings have important implications for the prioritization of clinical measures used to identify patients with COVID-19 (and, potentially, other forms of acute respiratory distress syndrome) having an elevated risk of death.

Feature Importance Analysis and Machine Learning for Alzheimer's Disease Early Detection: Feature Fusion of the Hippocampus, Entorhinal Cortex, and Standardized Uptake Value Ratio.

Alzheimer's disease (AD) is a progressive neurological disorder characterized by mild memory loss and ranks as a leading cause of mortality in the USA, accounting for approximately 120,000 deaths per year. It is also the primary form of dementia. Early detection is critical for timely intervention as the neurodegenerative process often starts 15-20 years before cognitive symptoms manifest. This study focuses on determining feature importance in AD classification using fused texture features from 3D magnetic resonance imaging hippocampal and entorhinal cortex and standardized uptake value ratio (SUVR) derived from positron emission tomography (PET) images. To achieve this objective, we employed four distinct classifiers (Linear Support Vector Classification, Linear Discriminant Analysis, Logistic Regression, and Logistic Regression Classifier with Stochastic Gradient Descent Learning). These classifiers were used to derive both average and top-ranked importance scores for each feature based on their outputs. Our framework is designed to distinguish between two classes, AD-negative (or mild cognitive impairment stable [MCIs]) and AD-positive (or MCI conversion [MCIc]), using a probabilistic neural network classifier and the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The findings from the feature importance highlight the crucial role of the GLCM texture features extracted from the hippocampus and entorhinal cortex, demonstrating their superior performance compared to the volume and SUVR. GLCM texture AD classification achieved approximately 90% sensitivity in identifying MCIc cases while maintaining low false positives (below 30%) when fused with other features. Moreover, the receiver operating characteristic curves validate the GLCMs' superior performance in distinguishing between MCIs and MCIc. Additionally, fusing different types of features improved classification performance compared to relying solely on any single feature category. Our study emphasizes the pivotal role of GLCM texture features in early Alzheimer's detection.

Individualised prediction of resilience and vulnerability to sleep loss using EEG features.

It is well established that individuals differ in their response to sleep loss. However, existing methods to predict an individual's sleep-loss phenotype are not scalable or involve effort-dependent neurobehavioural tests. To overcome these limitations, we sought to predict an individual's level of resilience or vulnerability to sleep loss using electroencephalographic (EEG) features obtained from routine night sleep. To this end, we retrospectively analysed five studies in which 96 healthy young adults (41 women) completed a laboratory baseline-sleep phase followed by a sleep-loss challenge. After classifying subjects into sleep-loss phenotypic groups, we extracted two EEG features from the first sleep cycle (median duration: 1.6 h), slow-wave activity (SWA) power and SWA rise rate, from four channels during the baseline nights. Using these data, we developed two sets of logistic regression classifiers (resilient versus not-resilient and vulnerable versus not-vulnerable) to predict the probability of sleep-loss resilience or vulnerability, respectively, and evaluated model performance using test datasets not used in model development. Consistently, the most predictive features came from the left cerebral hemisphere. For the resilient versus not-resilient classifiers, we obtained an average testing performance of 0.68 for the area under the receiver operating characteristic curve, 0.72 for accuracy, 0.50 for sensitivity, 0.84 for specificity, 0.61 for positive predictive value, and 3.59 for likelihood ratio. We obtained similar performance for the vulnerable versus not-vulnerable classifiers. These results indicate that logistic regression classifiers based on SWA power and SWA rise rate from routine night sleep can largely predict an individual's sleep-loss phenotype.

Tongue-Coating Microbial and Metabolic Characteristics in Halitosis

Halitosis is a common oral condition, which leads to social embarrassment and affects quality of life. Cumulative evidence has suggested the association of tongue-coating microbiome with the development of intraoral halitosis. The dynamic variations of tongue-coating microbiota and metabolites in halitosis have not been fully elucidated. Therefore, the present study aimed to determine the tongue-coating microbial and metabolic characteristics in halitosis subjects without other oral diseases using metagenomics and metabolomics analysis. The participants underwent oral examination, halitosis assessment, and tongue-coating sample collection for the microbiome and metabolome analysis. It was found that the microbiota richness and diversity were significantly elevated in the halitosis group. Furthermore, species from Actinomyces, Prevotella, Veillonella, and Solobacterium were significantly more abundant in the halitosis group. However, the Rothia and Streptococcus species exhibited opposite tendencies. Eleven Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched in the halitosis tongue coatings, including cysteine and methionine metabolism. Functional genes related to sulfur, indole, skatole, and cadaverine metabolic processes (such as serA, metH, metK and dsrAB) were identified to be more abundant in the halitosis samples. The metabolome analysis revealed that indole-3-acetic, ornithine, and L-tryptophan were significantly elevated in the halitosis samples. Furthermore, it was observed that the values of volatile sulfur compounds and indole-3-acetic abundances were positively correlated. The multiomics analysis identified the metagenomic and metabolomic characteristics to differentiate halitosis from healthy individuals using the least absolute shrinkage and selection operator logistic regression and random forest classifier. A total of 19 species and 39 metabolites were identified as features in halitosis patients, which included indole-3-acetic acid, Bacillus altitudinis, Candidatus Saccharibacteria, and Actinomyces species. In conclusion, an evident shift in microbiome and metabolome characteristics was observed in the halitosis tongue coating, which may have a potential etiological significance and provide novel insights into the mechanism for halitosis.

Contrast Agent Dynamics Determine Radiomics Profiles in Oncologic Imaging.

The reproducibility of radiomics features extracted from CT and MRI examinations depends on several physiological and technical factors. The aim was to evaluate the impact of contrast agent timing on the stability of radiomics features using dynamic contrast-enhanced perfusion CT (dceCT) or MRI (dceMRI) in prostate and lung cancers. Radiomics features were extracted from dceCT or dceMRI images in patients with biopsy-proven peripheral prostate cancer (pzPC) or biopsy-proven non-small cell lung cancer (NSCLC), respectively. Features that showed significant differences between contrast phases were identified using linear mixed models. An L2-penalized logistic regression classifier was used to predict class labels for pzPC and unaffected prostate regions-of-interest (ROIs). Nine pzPC and 28 NSCLC patients, who were imaged with dceCT and/or dceMRI, were included in this study. After normalizing for individual enhancement patterns by defining seven individual phases based on a reference vessel, 19, 467 and 128 out of 1204 CT features showed significant temporal dynamics in healthy prostate parenchyma, prostate tumors and lung tumors, respectively. CT radiomics-based classification accuracy of healthy and tumor ROIs was highly dependent on contrast agent phase. For dceMRI, 899 and 1027 out of 1118 features were significantly dependent on time after contrast agent injection for prostate and lung tumors. CT and MRI radiomics features in both prostate and lung tumors are significantly affected by interindividual differences in contrast agent dynamics.

Optimizing breast cancer diagnosis with photoacoustic imaging: An analysis of intratumoral and peritumoral radiomics

BackgroundThe differentiation between benign and malignant breast tumors extends beyond morphological structures to encompass functional alterations within the nodules. The combination of photoacoustic (PA) imaging and radiomics unveils functional insights and intricate details that are imperceptible to the naked eye. PurposeThis study aims to assess the efficacy of PA imaging in breast cancer radiomics, focusing on the impact of peritumoral region size on radiomic model accuracy. Materials and methodsFrom January 2022 to November 2023, data were collected from 358 patients with breast nodules, diagnosed via PA/US examination and classified as BI-RADS 3–5. The study used the largest lesion dimension in PA images to define the region of interest, expanded by 2 mm, 5 mm, and 8 mm, for extracting radiomic features. Techniques from statistics and machine learning were applied for feature selection, and logistic regression classifiers were used to build radiomic models. These models integrated both intratumoral and peritumoral data, with logistic regressions identifying key predictive features. ResultsThe developed nomogram, combining 5 mm peritumoral data with intratumoral and clinical features, showed superior diagnostic performance, achieving an AUC of 0.950 in the training cohort and 0.899 in validation. This model outperformed those based solely on clinical features or other radiomic methods, with the 5 mm peritumoral region proving most effective in identifying malignant nodules. ConclusionThis research demonstrates the significant potential of PA imaging in breast cancer radiomics, especially the advantage of integrating 5 mm peritumoral with intratumoral features. This approach not only surpasses models based on clinical data but also underscores the importance of comprehensive radiomic analysis in accurately characterizing breast nodules.

PseUpred-ELPSO Is an Ensemble Learning Predictor with Particle Swarm Optimizer for Improving the Prediction of RNA Pseudouridine Sites.

RNA pseudouridine modification exists in different RNA types of many species, and it has a significant role in regulating the expression of biological processes. To understand the functional mechanisms for RNA pseudouridine sites, the accurate identification of pseudouridine sites in RNA sequences is essential. Although several fast and inexpensive computational methods have been proposed, the challenge of improving recognition accuracy and generalization still exists. This study proposed a novel ensemble predictor called PseUpred-ELPSO for improved RNA pseudouridine site prediction. After analyzing the nucleotide composition preferences between RNA pseudouridine site sequences, two feature representations were determined and fed into the stacking ensemble framework. Then, using five tree-based machine learning classifiers as base classifiers, 30-dimensional RNA profiles are constructed to represent RNA sequences, and using the PSO algorithm, the weights of the RNA profiles were searched to further enhance the representation. A logistic regression classifier was used as a meta-classifier to complete the final predictions. Compared to the most advanced predictors, the performance of PseUpred-ELPSO is superior in both cross-validation and the independent test. Based on the PseUpred-ELPSO predictor, a free and easy-to-operate web server has been established, which will be a powerful tool for pseudouridine site identification.