Least Absolute Shrinkage And Selection Operator Research Articles

Integrating intratumoral and peritumoral radiomics with clinical risk factors for prognostic prediction in pancreatic ductal adenocarcinoma patients undergoing combined chemotherapy and HIFU ablation

Objective A radiomics nomogram will be created utilizing MRI data from intratumoral and peritumoral areas to forecast survival outcomes in patients who have had treatment for pancreatic ductal adenocarcinoma (PDAC). Methods A total of 87 individuals diagnosed with PDAC were included in the study, with 60 patients in the training cohort and 27 patients in the validation cohort. A grand total of 2395 radiomics characteristics were extracted from the tumor region and the peritumoral region. The least absolute shrinkage and selection operator (LASSO) method was used to select features and create a radiomics score, also known as the Rad-score. A multivariate regression analysis was then conducted to build the radiomics nomogram. The evaluation of the nomogram included discrimination, calibration, and clinical utility assessments. Results Based on the conclusions derived from the multivariate Cox model, Rad-Score, jaundice, and tumor size were identified as independent risk factors for overall survival (OS). The inclusion of the Rad-score in the radiomics nomogram led to improved accuracy in predicting survival compared to the clinical model. Patients were categorized into high-risk and low-risk groups based on their Rad-Score. Kaplan-Meier analysis revealed a statistically significant difference between the two groups (p < 0.05). Furthermore, the radiomics nomogram demonstrated excellent ability to differentiate, calibrate, and provide clinical utility in both the training and validation groups. Conclusions The MRI-based intratumoral and peritumoral radiomics nomogram, integrating the Rad-score and clinical data, provided better prognostic prediction for PDAC patients after HIFU treatment, which may hold great potential for guiding personalized care for these patients.

Risk signature of NETosis-related subtype predicts prognosis and evaluates immunotherapy effectiveness in gastric cancer.

Gastric cancer (GC) has a high incidence and mortality rate with a poor prognosis, so it is crucial to search for new biomarkers. The role of NETosis, a newly identified type of programmed cell death, in GC and its underlying mechanisms have yet to be explored and still require thorough investigation. Our research seeks to enhance our comprehension of NETosis and may offer novel approaches for treating GC. Utilizing The Cancer Genome Atlas-stomach adenocarcinoma (TCGA-STAD) dataset for training and the GSE84433 dataset for validation, our study delved into the associations between NETosis-related genes and the clinical risk of GC. Through comprehensive clustering, enrichment, and immune infiltration analyses, we evaluated the prognostic relevance of these NETosis genes in vivo. Furthermore, we devised a NETosis-related risk signature (NRRS) to assess its implications in risk stratification, survival prognosis, immune infiltration, and drug sensitivity. The NRRS's accuracy was validated by immunohistochemical staining. By applying consensus clustering to data from 62 NETosis-related genes, we categorized patients into two distinct subgroups, C1 and C2. These subgroups demonstrated significant differences. Following this, we developed the NRRS using the least absolute shrinkage and selection operator (LASSO) regression analysis. This process involved the selection of the following genes: CXCR4, NRP1, PDCD1, CTLA4, AKR1B1, SERPINE1, RGS2, SLCO2A1, TNFAIP2, RNASE1, DOC2B, APOD, ENTPD2, and CCL24. High-risk and low-risk groups can be accurately distinguished. We further verify in the verification set. These results suggest that NETosis is related to the microenvironment of GC. Our designed NRRS can predict the survival of patients with GC. We emphasized the relationship between NETosis and GC. We built and validated the value of NRRS. This contributes to deepening our view of NETosis and potentially provides new strategies for GC treatment.

Pathomics signatures and cuproptosis-related genes signatures for prediction of prognosis in patients with hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a common malignant tumor with high heterogeneity and poor prognosis, so early prediction and treatment are still difficult. Cuproptosis is a newly discovered type of programmed cell death that has been shown to be closely related to the occurrence and progression of HCC. Cancer morphology is influenced by genetic drivers, and computational pathology methods typically use tissue images such as entire slide images as input to predict clinical or genetic features. Therefore, the comprehensive analysis of pathological features and genomic data provides a feasible way to explore the potential mechanism of the tumor. The objective of this study was to develop a prediction model for HCC prognosis based on the pathomics signatures (PS) and the genomics signatures (GS). A dataset comprising 315 HCC patients was randomly divided into a training set (n=200) and a validation set (n=115). Prognostic models related to PS and GS were constructed by univariate and multivariate Cox regression analyses and least absolute shrinkage and selection operator (LASSO) regression analysis. Kaplan-Meier survival analysis, receiver operating characteristic (ROC) curve, univariate and multivariate Cox analyses, and nomogram were used to evaluate the predictive performance of the prognostic model. The prognostic value of the model was internally validated. A prognostic model incorporating clinical features, PS, and GS was developed using Cox regression analysis and LASSO regression analyses. Kaplan-Meier survival analysis revealed statistically significant differences in survival time between high-risk and low-risk subgroups in both the training and validation datasets (PS: P=0.003 and <0.001, respectively; GS: P=0.008 and 0.004, respectively). The time-dependent ROC curve showed favorable predictive value for survival in both the training and validation sets. The area under the ROC curves at 1, 3, and 5 years was 0.750, 0.830, and 0.870 in the training set, and 0.780, 0.810, and 0.760 in the validation set, respectively. A nomogram model based on the risk model score could effectively predict the survival probability of HCC patients. The calibration curves further demonstrated the good predictive capability of the nomogram model. The prognostic model incorporating PS and GS could effectively predict the prognosis of HCC patients.

Decoding the immune microenvironment: unveiling CD8 + T cell-related biomarkers and developing a prognostic signature for personalized glioma treatment

BackgroundGliomas are aggressive brain tumors with poor prognosis. Understanding the tumor immune microenvironment (TIME) in gliomas is essential for developing effective immunotherapies. This study aimed to identify TIME-related biomarkers in glioma using bioinformatic analysis of RNA-seq data.MethodsIn this study, we employed weighted gene co-expression network analysis (WGCNA) on bulk RNA-seq data to identify TIME-related genes. To identify prognostic genes, we performed univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. Based on these genes, we constructed a prognostic signature and delineated risk groups. To validate the prognostic signature, external validation was conducted.ResultsCD8 + T cell infiltration was strongly correlated with glioma patient prognosis. We identified 115 CD8 + T cell-related genes through integrative analysis of bulk-seq data. CDCA5, KIF11, and KIF4A were found to be significant immune-related genes (IRGs) associated with overall survival in glioma patients and served as independent prognostic factors. We developed a prognostic nomogram that incorporated these genes, age, gender, and grade, providing a reliable tool for clinicians to predict patient survival probabilities. The nomogram’s predictions were supported by calibration plots, further validating its accuracy.ConclusionIn conclusion, our study identifies CD8 + T cell infiltration as a strong predictor of glioma patient outcomes and highlights the prognostic value of genes. The developed prognostic nomogram, incorporating these genes along with clinical factors, provides a reliable tool for predicting patient survival probabilities and has important implications for personalized treatment decisions in glioma.

Machine learning model to predict early recurrence in patients with perihilar cholangiocarcinoma planned treatment with curative resection: a multicenter study

BackgroundEarly recurrence is the leading cause of death for patients with perihilar cholangiocarcinoma (pCCA) after surgery. Identifying high-risk patients preoperatively is important. This study aimed to construct a preoperative prediction model for the early recurrence of patients with pCCA to facilitate planned treatment with curative resection. MethodsThis study ultimately enrolled 400 patients with pCCA after curative resection in 5 hospitals between 2013 and 2019. They were randomly divided into training (n = 300) and testing groups (n = 100) at a ratio of 3:1. Associated variables were identified via least absolute shrinkage and selection operator (LASSO) regression. Four machine learning models were constructed: support vector machine, random forest (RF), logistic regression, and K-nearest neighbors. The predictive ability of the models was evaluated via receiving operating characteristic (ROC) curves, precision-recall curve (PRC) curves, and decision curve analysis. Kaplan-Meier (K-M) survival curves were drawn for the high-/low-risk population. ResultsFive factors: carbohydrate antigen 19–9, tumor size, total bilirubin, hepatic artery invasion, and portal vein invasion, were selected by LASSO regression. In both the training and testing groups, the ROC curve (area under the curve: 0.983 vs 0.952) and the PRC (0.981 vs 0.939) showed that RF was the best. The cutoff value for distinguishing high- and low-risk patients was 0.51. K-M survival curves revealed that in both groups, there was a significant difference in RFS between high- and low-risk patients (P < .001). ConclusionThis study used preoperative variables from a large, multicenter database to construct a machine learning model that could effectively predict the early recurrence of pCCA in patients to facilitate planned treatment with curative resection and help clinicians make better treatment decisions.

Radiomics model for predicting distant metastasis in soft tissue sarcoma of the extremities and trunk treated with surgery.

The aim of this study was to develop a radiomics model based on magnetic resonance imaging (MRI) for predicting metastasis in soft tissue sarcomas (STSs) treated with surgery. MRI and clinical data of 73 patients with STSs of the extremities and trunk were obtained from TCIA database and Jiangsu Cancer Hospital as the training set, data of other 40 patients were retrospectively collected at our institution as the external validation set. Radiomics features were extracted from both intratumoral and peritumoral regions of fat-suppressed T2-weighted images (FS-T2WIs) of patients, and 3D ResNet10 was used to extract deep learning features. Recursive feature elimination (RFE) and least absolute shrinkage and selection operator (LASSO) algorithms were used for the selection of features. Based on 4 different sets of features, 5 machine learning algorithms were used to construct intratumor, peritumor, combined intratumor and peritumor radiomics models and deep learning radiomics (DLR) model. The area under the ROC curve (AUC) and Decision curve analysis (DCA) were used to evaluate the ability of models to predict metastasis. Based on 20 selected features from the deep-learning and radiomics features set, the DLR model was able to predict metastasis in the validation dataset, with an AUC of 0.9770. The DCA and Hosmer-Lemeshow test revealed that the DLR model had good clinical benefit and consistency. By getting richer information from MRI, The DLR model is a noninvasive, low-cost method for predicting the risk of metastasis in STSs, and can help develop appropriate treatment programs.

Identification and RT-qPCR Validation of Biomarkers Based on Butyrate Metabolism-Related Genes to Predict Recurrent Miscarriage.

To date, the cause of recurrent miscarriage (RM) in at least 50% of patients remains unknown. However, no study has explored the correlation between butyrate metabolism-related genes (BMRGs) and RM. RM-related datasets (GSE165004, GSE111974, GSE73025, and GSE179996) were obtained from the Gene Expression Omnibus (GEO) database. First, 595 differentially expressed genes (DEGs) were identified between the RM and control samples in GSE165004. Subsequently, 213 differentially expressed BMRGs (DE-BMRGs) were identified by considering the intersection of DEGs with BMRGs. The protein-protein interaction (PPI)network of DE-BMRGs contained 156 nodes and 250 edges, and a key module was obtained. In total, four biomarkers (ACTR2, ANXA2, PFN1, and OAS1) were acquired through least absolute shrinkage and selection operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and random forest (RF). Immune analysis revealed two immune cells and three immune-related gene sets that were significantly different between the RM and control groups, namely, T helper cells, regulatory T cells (Treg), MHC class I, parainflammation, and type I IFN response. In addition, a TF-mRNA network based on the top 100 nodes ranked in the order of connectivity was created, including 100 nodes and 253 edges, such as MTERF2-ACTR2, NKX23-PFN1, STAT1-OAS1, and SP100-ANXA2. Finally, 3 drugs (withaferin A, N-ethylmaleimide, and etoposide) were predicted to interact with 2 biomarkers (ANXA2 and ACTR2). Eventually, ANXA2 and OAS1 were significantly downregulated, and PFN1 was markedly overexpressed in the RM group, as determined by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Our findings authenticated four butyrate metabolism-related biomarkers for the diagnosis of RM, providing a scientific reference for further studies on RM treatment.

Using artificial intelligence based imaging to predict lymph node metastasis in non-small cell lung cancer: a systematic review and meta-analysis.

Lung cancer, especially non-small cell lung cancer (NSCLC), is one of the most-deadly malignancies worldwide. Lung cancer has a worse 5-year survival rate than many primary malignancies. Thus, the early detection and prognosis prediction of lung cancer are crucial. The early detection and prognosis prediction of lung cancer have improved with the widespread use of artificial intelligence (AI) technologies. This meta-analysis examined the accuracy and efficacy of AI-based models in predicting lymph node metastasis (LNM) in NSCLC patients using imaging data. Our findings could help clinicians predict patient prognosis and select alternative therapies. We searched the PubMed, Web of Science, Cochrane Library, and Embase databases for relevant articles published up to January 31, 2024. Two reviewers individually evaluated all the retrieved articles to assess their eligibility for inclusion in the meta-analysis. The systematic assessment and meta-analysis comprised articles that satisfied the inclusion criteria (e.g., randomized or non-randomized trials, and observational studies) and exclusion criteria (e.g., articles not published in English), and provided data for the quantitative synthesis. The quality of the included articles was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2). The pooled sensitivity, specificity, and area under the curve (AUC) were used to evaluate the ability of AI-based imaging models to predict LNM in NSCLC patients. Sources of heterogeneity were investigated using meta-regression. Covariates, including country, sample size, imaging modality, model validation technique, and model algorithm, were examined in the subgroup analysis. The final meta-analysis comprised 11 retrospective studies of 6,088 NSCLC patients, of whom 1,483 had LNM. The pooled sensitivity, specificity, and AUC of the AI-based imaging model for predicting LNM in NSCLC patients were 0.87 [95% confidence interval (CI): 0.80-0.91], 0.85 (95% CI: 0.78-0.89), and 0.92 (95% CI: 0.90-0.94). Based on the QUADAS-2 results, a risk of bias was detected in the patient selection and diagnostic tests of the included articles. However, the quality of the included articles was generally acceptable. The pooled sensitivity and specificity were heterogeneous (I2>75%). The meta-regression and subgroup analyses showed that imaging modality [computed tomography (CT) or positron emission tomography (PET)/CT], and the neural network method model design significantly affected heterogeneity of this study. Models employing sample size data from a single center and the least absolute shrinkage and selection operator (LASSO) method had greater sensitivity than other techniques. Using the Deek' s funnel plot, no publishing bias was found. The results of the sensitivity analysis showed that deleting each article one by one did not change the findings. Imaging data models based on AI algorithms have good diagnostic accuracy in predicting LNM in patients with NSCLC and could be applied in clinical settings.

Brain metastases in newly diagnosed lung cancer: epidemiology and conditional survival.

The brain serves as the primary site for metastasis in patients with both non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). The presence of lung cancer with brain metastasis (LCBM) is a debilitating condition associated with considerable morbidity and mortality. The objective of this study was to assess the incidence and survival rates of LCBM in the United States population. We analyzed a total of 9,212 patients diagnosed with LCBM between 2010 and 2015, extracted from the Surveillance, Epidemiology, and End Results (SEER) database. Our analysis assessed the incidence, relative survival, and conditional survival (CS) of LCBM. We utilized the Kaplan-Meier method to estimate overall survival and determine CS at year y+x after x years of survival, following the formula CS(y|x) = CS(y+x)/CS(x). Prognostic factor selection was performed using the least absolute shrinkage and selection operator (LASSO) regression approach, and multivariate Cox regression was employed to demonstrate the impact of these predictors on outcomes and construct a CS-based nomogram. The overall age-adjusted incidence rate of LCBM was 5.82 cases per 100,000, with a slight decline observed during our study period. Patient relative survival showed a continuous decline with increasing age. CS analysis revealed that the 5-year CS rate for patients initially diagnosed with LCBM adjusted from 3% to 13%, 28%, 52%, and 73% over successive years of survival (1-4 years). Identified predictors included age at diagnosis, sex, race, tumor size, tumor grade, surgery, radiotherapy, and chemotherapy. These predictors, along with the CS formula, were employed to develop a CS-based nomogram for real-time prognosis prediction. Calibration curve, area under the time-dependent receiver operating characteristic (ROC) curve, concordance index (c-index), and decision curve analysis (DCA) demonstrated the model's strong predictive capabilities. This study deepened our understanding of LCBM patients, summarizing their epidemiological characteristics and CS patterns. We successfully developed a novel CS-based nomogram model for dynamic survival estimation, offering real-time and personalized prognostic information that is clinically valuable.

Establishment and verification of a prognostic immune cell signature-based model for breast cancer overall survival.

Breast cancer (BRCA) is a prevalent and aggressive disease. Despite various treatments being applied, a significant number of patients continue to experience unfavorable prognoses. Accurate prognosis prediction in BRCA is crucial for tailoring individualized treatment plans and improving patient outcomes. Recent studies have highlighted the significance of immune cell infiltration in the tumor microenvironment (TME), but predicting survival remains challenging due to the heterogeneity of BRCA. The aim of this study was thus to produce an immune cell signature-based framework capable of predicting the prognosis of patients with BRCA. The GSE169246 dataset was from the Gene Expression Omnibus (GEO) database, comprising single-cell RNA sequencing (scRNA-seq) data from 95 individuals with BRCA. Seurat, principal component analysis (PCA), the unified matrix polynomial approach (UMAP) algorithm, and linear dimensionality reduction were used to determine the heterogeneity of T cells. Overlapping analysis of differentially expressed genes (DEGs), genes associated with prognosis, and T-cell pharmacodynamics-related genes were used to obtain the T-cell core pharmacodynamics-related genes. The dimensionality of the T-cell core pharmacodynamics-related genes was reduced employing the least absolute shrinkage and selection operator (LASSO) Cox regression model and the LASSO model. The prognostic model was built via a Cox analysis of the overall survival (OS) information. The clinical sample included 95 patients with BRCA who underwent surgical treatment from October 2018 to October 2021 at the Second Affiliated Hospital of Qiqihar Medical University. Patients were divided into a good prognosis group and a poor prognosis group based on their prognostic outcomes. The predictive value of tumor characteristics and immune responses was validated through correlation analysis, logistic regression analysis, and receiver operating characteristic (ROC) analysis. A group of 95 genes was used to establish a prognostic model. In the GEO clinical sample, with a high-risk group demonstrating shorter median survival times (2,447 vs. 6,498 days, P=4.733e-12). Area under the curve (AUC) values of 0.75, 0.75, and 0.72 were obtained for 2-, 4-, and 6-year OS predictions, respectively. Clinical validation found that the 6-year OS of the favorable prognosis group was significantly higher than that of the unfavorable prognosis group (92.06% vs. 65.62%; P=0.005). Poor prognosis was positively correlated with age, tumor size, B-cell level, and CTLA4 level and negatively correlated with tumor stage (T1/T2), lymph node metastasis stage (N0), clinical stage I-II, CD3+T-cell, CD4+T-cell, CD8+T-cell, neutrophil, lymphocyte, natural kill cell, TIGIT expression and OS. The combined model of clinical parameters had an AUC value of 0.898. This study established a prognostic model that demonstrated excellent predictive value for OS of BRCA. The predictive model developed offers valuable insights into prognosis and treatment planning, emphasizing the importance of tumor characteristics and immune cell infiltration.

Identifying functional cuproptosis-related long non-coding RNAs in patients with bladder cancer.

Bladder cancer is the most common malignancy of the urinary tract and one of the most common cancers in the world. Cuproptosis is a novel type of cell death associated with tumorigenesis. In this study, we assessed the correlation between cuproptosis-related genes and tumorigenesis. Moreover, we constructed a prognostic signature. Pearson correlation analysis and univariate Cox regression were utilized to extract cuproptosis-related long non-coding RNAs (lncRNAs) predicting prognosis in The Cancer Genome Atlas (TCGA) database. The least absolute shrinkage and selection operator (LASSO) Cox regression was utilized to establish a cuproptosizs-related prognostic signature. A nomogram signature was generated to predict individual survival. We obtained 19 cuproptosis-related genes and 14 prognostic cuproptosis-related lncRNAs. We constructed a seven-prognostic risk signature. Time-dependent receiver operating characteristic (ROC) curves demonstrated good predictive power (1-, 3-, and 5-year survival rates of 0.711, 0.673, and 0.684, respectively). The high-risk group reported a worse prognosis than the low-risk group, and the risk signature was identified as an independent factor. The biological process of risk-related genes primarily involved tumorigenesis and migration. The high-risk group expressed high chemokines and T cell inhibition and low antigen-presenting cells. Cuproptosis-related lncRNAs are central to tumorigenesis, providing a novel therapeutic target for patients with bladder cancer. We constructed an individualized predictive signature based on cuproptosis-related lncRNAs.

Machine learning study of universal electronic stopping cross-sections of ions in matter

Accurate electronic stopping cross-section (ESCS) database of ions in matter is crucial for precise simulation of radiation damage. Based on the experimental-cleaned database of SRIM, binary theory and unitary convolution approximation as well as the descriptor pool extracted from these models, we developed a universal machine learning ESCS database using the least absolute shrinkage and selection operator (LASSO) algorithm. This method allows for predictions for ion-target combinations with atomic numbers from 1 to 92, within the energy range from 1 keV/u to 1 GeV/u, addressing the limitations of machine learning on training dataset. The database exhibits remarkable accuracy in predicting ESCS and ion depth distribution/range, along with robust reciprocity performance. Key descriptors are also determined, which closely mimic the Lindhard-Scharff-Schiott and Bohr-Bethe-Bloch formulations, achieved through precise adjustments of the exponent of individual elements. The proposed universal ESCS database surpasses the accuracy of existing databases, supporting related applications across a wide range of energies and systems.

Integrating Bioinformatics and Experimental Validation to Identify Mitochondrial Permeability Transition-Driven Necrosis-Related lncRNAs that can Serve as Prognostic Biomarkers and Therapeutic Targets in Endometrial Carcinoma.

Endometrial carcinoma (EC) is a common malignant tumor in women with high mortality and relapse rates. Mitochondrial permeability transition (MPT)-driven necrosis is a novel form of programmed cell death. The MPT-driven necrosis related lncRNAs (MRLs) involved in EC development remain unclear. We aimed to predict the outcomes of patients with EC by constructing a novel prognostic model based on MRLs and explore potential molecular functions. A risk prognostic model was developed utilizing multi-Cox regression in conjunction with the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm, which was based on MRLs. The predictive efficacy of the model was evaluated through receiver operating characteristic (ROC) curve analysis, as well as nomogram and concordance index (C-index) assessments. Patients were categorized into high- and low-risk groups based on their median risk scores. Notably, the high-risk group exhibited significantly poorer overall survival (OS) outcomes. Gene ontology (GO) and Gene set enrichment analysis (GSEA) demonstrated that Hedgehog and cell cycle pathways were enriched in the high-risk group. Tumor Immune Dysfunction and Exclusion (TIDE) displayed that patients in the high-risk group showed a high likelihood of immune evasion and less effective immunotherapy. A significant disparity in immune function was also observed between two groups. Based on the nine-MRLs, drug sensitivity analysis identified several anticancer drugs with potential efficacy in prognosis. Meanwhile, the results demonstrated that OGFRP1 plays a carcinogenic role by affecting mitochondrial membrane permeability in EC. Therefore, the risk model constructed by nine MRLs could be used to predict the clinical outcomes and therapeutic responses in patients with EC effectively.

Bayesian estimation and comparison of idiographic network models.

Idiographic network models are estimated on time series data of a single individual and allow researchers to investigate person-specific associations between multiple variables over time. The most common approach for fitting graphical vector autoregressive (GVAR) models uses least absolute shrinkage and selection operator (LASSO) regularization to estimate a contemporaneous and a temporal network. However, estimation of idiographic networks can be unstable in relatively small data sets typical for psychological research. This bears the risk of misinterpreting differences in estimated networks as spurious heterogeneity between individuals. As a remedy, we evaluate the performance of a Bayesian alternative for fitting GVAR models that allows for regularization of parameters while accounting for estimation uncertainty. We also develop a novel test, implemented in the tsnet package in R, which assesses whether differences between estimated networks are reliable based on matrix norms. We first compare Bayesian and LASSO approaches across a range of conditions in a simulation study. Overall, LASSO estimation performs well, while a Bayesian GVAR without edge selection may perform better when the true network is dense. In an additional simulation study, the novel test is conservative and shows good false-positive rates. Finally, we apply Bayesian estimation and testing in an empirical example using daily data on clinical symptoms for 40 individuals. We additionally provide functionality to estimate Bayesian GVAR models in Stan within tsnet. Overall, Bayesian GVAR modeling facilitates the assessment of estimation uncertainty which is important for studying interindividual differences of intraindividual dynamics. In doing so, the novel test serves as a safeguard against premature conclusions of heterogeneity. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Identifying Brain Network Structure for an fMRI Effective Connectivity Study Using the Least Absolute Shrinkage and Selection Operator (LASSO) Method.

Background: Studying causality relationships between different brain regions using the fMRI method has attracted great attention. To investigate causality relationships between different brain regions, we need to identify both the brain network structure and the influence magnitude. Most current methods concentrate on magnitude estimation, but not on identifying the connection or structure of the network. To address this problem, we proposed a nonlinear system identification method, in which a polynomial kernel was adopted to approximate the relation between the system inputs and outputs. However, this method has an overfitting problem for modelling the input-output relation if we apply the method to model the brain network directly. Methods: To overcome this limitation, this study applied the least absolute shrinkage and selection operator (LASSO) model selection method to identify both brain region networks and the connection strength (system coefficients). From these coefficients, the causality influence is derived from the identified structure. The method was verified based on the human visual cortex with phase-encoded designs. The functional data were pre-processed with motion correction. The visual cortex brain regions were defined based on a retinotopic mapping method. An eight-connection visual system network was adopted to validate the method. The proposed method was able to identify both the connected visual networks and associated coefficients from the LASSO model selection. Results: The result showed that this method can be applied to identify both network structures and associated causalities between different brain regions. Conclusions: System identification with LASSO model selection algorithm is a powerful approach for fMRI effective connectivity study.

Constructing a predictive model based on peripheral blood signs to differentiate infectious mononucleosis from chronic active EBV infection.

To develop a prediction model based on peripheral blood signs to distinguish between infectious mononucleosis and chronic active EBV infection. Retrospective data was collected for 60 patients with IM (IM group) and 20 patients with CAEBV infection (CAEBV group) who were hospitalized and diagnosed at the General Hospital of Tianjin Medical University between December 2018 and September 2022. The analyses used were univariate and LASSO (least absolute shrinkage and selection operator) logistic regression. Univariate analyses revealed that both IM and CAEBV-infected patients displayed overlapping and intersecting clinical manifestations, such as fever, sore throat, enlarged lymph nodes, and enlargement of the liver and spleen, and that in contrast to inflammatory responses in peripheral blood, CAEBV-infected patients had more severe inflammatory responses. Nine biomarkers-HGB, lymphocyte count, percentage of lymphocytes, ALB, fibrinogen, CRP, IFN-, IL-6, and EBV-DNA load-were subsequently selected by LASSO logistic regression modeling to serve as discriminatory models. Our investigation offers a solid foundation for diagnosing IM and CAEBV infection using the LASSO logistic regression model based on the significance and availability of peripheral blood indicators. Infected patients with CAEBV require early medical attention.

Development and validation of a recurrence risk assessment model for high-grade bladder cancer based on TCGA and GEO.

Bladder cancer is one of the most commonly diagnosed urinary cancers worldwide. Although muscle-invasive bladder cancer (MIBC) accounts for only 25% of bladder cancer cases, it has a high recurrence rate and poor prognosis, especially among high-grade cases. Despite the existence of some molecular markers, there is a clear clinical need for a robust recurrence prediction model that can assist in patient management and therapeutic decision-making. Therefore, we aimed to use public databases to develop such an effective assessment model. We developed a recurrence risk assessment model for high-grade bladder cancer based on the clinical information of 217 cases from The Cancer Genome Atlas (TCGA) and profiles of 87 samples from GSE31684 in the Gene Expression Omnibus (GEO) database. Edge R was used to analyze differences between RNAs of bladder cancer in the TCGA database, with thresholds of P<0.05 and |log2(fold change)| >1; least absolute shrinkage and selection operator (LASSO) Cox regression models were used to screen the RNAs significantly related to recurrence with minimum λ. Survival receiver operating characteristic (ROC) and area under the curve (AUC) was used to assess the predictive accuracy of the model in the training and validation sets of GSE31684. There were 2,876 differential RNAs obtained from TCGA data. Among a total of 284 RNAs identified as significantly related to recurrence of bladder cancer, 49 were obtained by LASSO regression, and 30 were finally obtained by multifactor risk regression to construct a risk assessment model. The model was found to predict the prognosis of bladder cancer recurrence well, with an AUC of 0.911 in the TCGA training set and an adjusted AUC value of 0.839 in the GEO validation set. The recurrence assessment model is a relatively accurate recurrence prediction tool for high-grade bladder cancer and could provide a guidance for the treatment of bladder cancer.

Gender differences in Chinese Adolescents’ school refusal: A network analysis to test the contribution of individual, family, and school factors

To better guide school practitioners in identifying and intervening with instances of school refusal, this study employs network analysis to investigate the core manifestations among adolescents of different genders and explores the impact of various ecological factors on these characteristics. In this study, 910 middle school students in China (Mage ± SDage = 13.55 ± 1.06, 48.13 % boys) were recruited to complete a paper-and-pencil survey on school refusal and its related factors. The least absolute shrinkage and selection operator (LASSO) method was used to examine the network characteristics of school refusal and the potential influence of ecological factors on the core characteristics of school refusal. Results revealed that: (1) the core features of Chinese students’ school refusal were “I consider studying a burden”, “I often try to find ways to avoid studying”, and “Studying often makes me feel inwardly tense and anxious”, demonstrating gender consistency; and (2) there were significant gender differences in the underlying ecological factors that influence the core characteristics of Chinese students’ school refusal. Specifically, boys’ school refusal is more related to their parental academic involvement and teacher expectations. The higher the parents’ academic involvement and teacher expectations, the lower the boys’ school refusal. Girls’ school refusal is more related to personal educational values ​​(the value of academic success and the future utility of education). The more girls identify with the value of education, the lower their school refusal. This study utilized network analysis to reveal unique gender differences in school refusal among Chinese adolescents. It also explored the complex interrelationships between individual, familial, and school factors and school refusal, demonstrating how these factors contribute differently in boys and girls. These findings indicated potential theoretical directions for future interventions for school refusal among Chinese students of different genders.

A Robust [18F]-PSMA-1007 Radiomics Ensemble Model for Prostate Cancer Risk Stratification.

The aim of this study is to investigate the role of [18F]-PSMA-1007 PET in differentiating high- and low-risk prostate cancer (PCa) through a robust radiomics ensemble model. This retrospective study included 143 PCa patients who underwent [18F]-PSMA-1007 PET/CT imaging. PCa areas were manually contoured on PET images and 1781 image biomarker standardization initiative (IBSI)-compliant radiomics features were extracted. A 30 times iterated preliminary analysis pipeline, comprising of the least absolute shrinkage and selection operator (LASSO) for feature selection and fivefold cross-validation for model optimization, was adopted to identify the most robust features to dataset variations, select candidate models for ensemble modelling, and optimize hyperparameters. Thirteen subsets of selected features, 11 generated from the preliminary analysis plus two additional subsets, the first based on the combination of robust and fine-tuning features, and the second only on fine-tuning features were used to train the model ensemble. Accuracy, area under curve (AUC), sensitivity, specificity, precision, and f-score values were calculated to provide models' performance. Friedman test, followed by post hoc tests corrected with Dunn-Sidak correction for multiple comparisons, was used to verify if statistically significant differences were found in the different ensemble models over the 30 iterations. The model ensemble trained with the combination of robust and fine-tuning features obtained the highest average accuracy (79.52%), AUC (85.75%), specificity (84.29%), precision (82.85%), and f-score (78.26%). Statistically significant differences (p < 0.05) were found for some performance metrics. These findings support the role of [18F]-PSMA-1007 PET radiomics in improving risk stratification for PCa, by reducing dependence on biopsies.

Development of a predictive model for the U-shaped relationship between the triglyceride glycemic index and depression using machine learning (NHANES 2009–2018)

BackgroundAt present, the relationship between depression and the triglyceride glycemic (TyG) index remains a topic of debate. This study sought to elucidate the relationship between depression and the TyG index to create a predictive model that would help doctors diagnose patients. MethodsWe conducted a cross-sectional study utilizing the National Health and Nutrition Examination Survey (NHANES) dataset, which comprises data from 2009 to 2018. The analysis involved 11,222 adults with a Patient Health Questionnaire-9 (PHQ-9) score of 5 or higher, indicating the presence of depression. As part of the analysis, multiple regression models were used to test whether a linear relationship existed between the TyG index and depression. A threshold effects analysis was used to generate smoothed curves and detect nonlinear correlations. Additionally, the Least Absolute Shrinkage and Selection Operator (LASSO) regression were employed to identify the key risk factors associated with depression. The factors identified were then used to construct the risk prediction nomogram. Finally, Receiver Operating Characteristic (ROC) curves were used to evaluate the discriminative performance of the model. ResultsMultivariable linear regression analysis indicated a strong positive correlation between depression and the TyG index (β: 0.38, 95 % CI: 0.16–0.60, p = 0.0008). A U-shaped relationship with an inflection point was observed at a TyG index of 8.16. The nomogram model, constructed using risk factors identified by LASSO, exhibited a significant predictive value (AUC = 0.888). ConclusionsThe results of this investigation point to a U-shaped association between depression risk and the TyG index among Americans. Those with a TyG index of over 8.16 are significantly more likely to develop depression. These results suggest a possible causal relationship and emphasize the importance of monitoring the TyG index in depression risk assessment.