Absolute Selection Research Articles

Characterizing adipocytokine-related signatures for prognosis prediction in prostate cancer

BackgroundProstate cancer (PCa) is a prevalent malignant tumor in males, with a significant incidence of biochemical recurrence (BCR) despite advancements in treatment. Adipose tissue surrounding the prostate, known as periprostatic adipose tissue (PPAT), contributes to PCa invasion through adipocytokine production. However, the relationship between adipocytokine-related genes and PCa prognosis remains understudied. This study was conducted to provide a theoretical basis and serve as a reference for the use of adipocytokine-related genes as prognostic markers in PCa.MethodsTranscriptome and survival data of PCa patients from The Cancer Genome Atlas (TCGA) database were analyzed. Differential gene expression analysis was conducted using the DESeq2 and limma packages. Prognostic genes were identified through univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression. A prognostic model was developed and validated utilizing receiver operating characteristic (ROC) and Kaplan-Meier (K-M) curves. Assessments of immune cell infiltration and drug sensitivity were also carried out. Subsequently, the function of BNIP3L gene in PCa was verified.ResultsA total of 47 adipocytokine-related differentially expressed genes (DEGs) were identified. Five genes (PPARGC1A, APOE, BNIP3L, STEAP4, and C1QTNF3) were selected as prognostic markers. The prognostic model demonstrated significant predictive accuracy in both training and validation cohorts. Patients with higher risk scores exhibited poorer survival outcomes. Immune cell infiltration analysis revealed that the high-risk group had increased immune and ESTIMATE scores, while the low-risk group had higher tumor purity. In vitro experiments confirmed the suppressive effects of BNIP3L on PCa cell proliferation, migration, and invasion.ConclusionThe prognostic model independently predicts the survival of patients with PCa, aiding in prognostic prediction and therapeutic efficacy. It expands the study of adipocytokine-related genes in PCa, presenting novel targets for treatment.

Primary diffuse large B-cell lymphoma of bone in adults: A SEER population-based study.

Primary diffuse large B-cell lymphoma of the bone (PB-DLBCL) is an extremely rare type of extra-nodal lymphoma. The clinical characteristics, management, and survival outcomes of adult PB-DLBCL patients remain poorly defined. To explore the clinical manifestations, staging, therapeutic options, prognostic factors and outcomes of adult patients with PB-DLBCL and to create a model to predict survival outcomes. Data of adult PB-DLBCL patients were obtained from the Surveillance, Epidemiology, and End Results (SEER) Program 18 registries database from 2000 to 2018. The Kaplan-Meier survival analysis was conducted to calculate survival rates. Univariate Cox regression, best subset selection (BESS), and least absolute shrinkage and selection operator (LASSO), followed by backward stepwise multivariable Cox regression, were used to construct the nomogram. The nomograms were evaluated using the concordance index (C-index), calibration curves and decision curve analysis (DCA). Diffuse large B-cell lymphoma (DLBCL) (67.51%) was the most frequent type of primary bone lymphoma. The most involved sites were the spine and lower-limb long bones. For the whole cohort, the 3-, 5-, 10- and 15-year overall survival (OS) rates were 74.9%, 70.5%, 60.0%, and 49.9%, and corresponding disease-specific survival (DSS) rates were 79.7%, 77.8%, 75.1%, and 71.4%, respectively. For OS, age, Ann Arbor stage, primary site and therapy were confirmed as final factors to develop the nomogram in adult PB-DLBCL patients, whereas for DSS, Age, marital status, Ann Arbor stage, number of bone lesions, therapy and year of diagnosis were confirmed as final factors in developing the nomogram. The nomograms demonstrated good accuracy and clinical utility. Established nomograms can accurately predict the survival of patients with PB-DLBCL and help clinicians optimize treatment.

Clinical-radiomics nomogram based on the fat-suppressed T2 sequence for differentiating luminal and non-luminal breast cancer

ObjectiveTo establish and validate a new clinical-radiomics nomogram based on the fat-suppressed T2 sequence for differentiating luminal and non-luminal breast cancer.MethodsA total of 593 breast cancer patients who underwent preoperative breast MRI from Jan 2017 to Dec 2020 were enrolled, which were randomly divided into the training (n=474) and test sets (n=119) at the ratio of 8:2. Intratumoral region (ITR) of interest were manually delineated, and peritumoral regions of 3 mm and 5 mm (PTR-3 mm and PTR-5 mm) were automatically obtained by dilating the ITR. Intratumoral and peritumoral radiomics features were extracted from the fat-suppressed T2-weighted images, including first-order statistical features, shape features, texture features, and filtered features. The Mann-Whitney U Test, Z score normalization, K-best method, and least absolute shrinkage and selection operator (LASSO) algorithm were applied to select key features to construct radscores based on ITR, PTR-3 mm, PTR-5 mm, ITR+PTR-3 mm and ITR+ PTR-5 mm. Risk factors were selected by univariate and multivariate logistic regressions and were used to construct a clinical model and a clinical-radiomics model that presented as a nomogram. The performance of models was assessed by sensitivity, specificity, accuracy, the area under the curve (AUC) of receiver operating characteristic (ROC), calibration curves, and decision curve analysis (DCA).ResultsITR+PTR-3 mm radsore and histological grade were selected as risk factors. A clinical-radiomics model was constructed by adding ITR+PTR-3mm radscore to the clinical factor, which was presented as a nomogram. The clinical-radiomics nomogram showed the highest AUC (0.873), sensitivity (72.3%), specificity (78.9%) and accuracy (77.0%) in the training set and the highest AUC (0.851), sensitivity (71.4%), specificity (79.8%) and accuracy (77.3%) in the test set. DCA showed that the clinical-radiomics nomogram had the greatest net clinical benefit compared to the other models.ConclusionThe clinical-radiomics nomogram showed promising clinical application value in differentiating luminal and non-luminal breast cancer.

Identification of metabolic biomarkers in idiopathic pulmonary arterial hypertension using targeted metabolomics and bioinformatics analysis

Pulmonary arterial hypertension (PAH) is a life-threatening disease with a poor prognosis, and metabolic abnormalities play a critical role in its development. This study used metabolomics, machine learning algorithms and bioinformatics to screen for potential metabolic biomarkers associated with the diagnosis of PAH. In this study, plasma samples were collected from 17 patients diagnosed with idiopathic pulmonary arterial hypertension (IPAH) and 20 healthy controls. Plasma metabolomic profiling was performed by high-performance liquid chromatography-mass spectrometry. Gene profiles of PAH patients were obtained from the GEO database. Key differentially expressed metabolites (DEMs) and metabolism-related genes were subsequently identified using machine learning algorithms. Twenty differential plasma metabolites associated with IPAH were identified (VIP score > 1 and p < 0 0.05), and enrichment analysis revealed the arginine biosynthesis pathway as the most altered pathway. Using machine learning models, including least absolute shrinkage and selection operator (LASSO), random forest (RF) and support vector machine (SVM), we extracted key metabolites that correlated with clinical phenotypes. Our results suggested that five metabolites, kynurenine, homoserine, tryptophan, AMP, and spermine, are potential biomarkers for IPAH. Bioinformatics analysis also identified 3 metabolism-related genes, MAPK6, SLC7A11 and CDC42BPA, that are strongly correlated with pulmonary hypertension, demonstrating strong predictive power and clinical relevance. Our findings revealed some key genes associated with metabolism in PH, and provided crucial information about complex metabolic reprogramming signals and may lead to the identification of useful metabolic biomarkers for the diagnosis of PAH.

Can we skip invasive biopsy of sentinel lymph nodes? A preliminary investigation to predict sentinel lymph node status using PET/CT-based radiomics

BackgroundSentinel lymph node (SLN) biopsy (SLNB) is considered the gold standard for detecting SLN metastases in patients with invasive ductal breast cancer (IDC). However, SLNB is invasive and associated with several complications. Thus, this study aimed to evaluate the diagnostic performance of a non-invasive radiomics analysis utilizing 2-deoxy-2-[18F]fluoro-d-glucose positron emission tomography/computed tomography (18F-FDG-PET/CT) for assessing SLN metastasis in IDC patients.MethodsThis retrospective study included 132 patients with biopsy-confirmed IDC, who underwent 18F-FDG PET/CT scans prior to mastectomy or breast-conserving surgery with SLNB. Tumor resection or SLNB was conducted within one-week post-scan. Clinical data and metabolic parameters were analyzed to identify independent SLN metastasis predictors. Radiomic features were extracted from each PET volume of interest (VOI) and CT-VOI. Feature selection involved univariate and multivariate logistic regression analysis, and the least absolute shrinkage and selection operator (LASSO) method. Three models were developed to predict SLN status using the random forest (RF), decision tree (DT), and k-Nearest Neighbors (KNN) classifiers. Model performance was assessed using the area under the receiver operating characteristic curve (AUC).ResultsThe study included 91 cases (32 SLN-positive and 59 SLN-negative patients) in the training cohort and 41 cases (29 SLN-positive and 12 SLN-negative patients) in the validation cohort. Multivariate logistic regression analysis identified Ki 67 and TLG as independent predictors of SLN status. Five PET-derived features, three CT-derived features, and two clinical variables were selected for model development. The AUC values of the RF, KNN, and DT models for the training cohort were 0.887, 0.849, and 0.824, respectively, and for the validation cohort were 0.856, 0.830, and 0.819, respectively. The RF model demonstrated the highest accuracy for the preoperative prediction of SLN metastasis in IDC patients.ConclusionThe PET-CT radiomics approach may offer robust and non-invasive predictors for SLN status in IDC patients, potentially aiding in the planning of personalized treatment strategies for IDC patients.

Association between visceral lipid accumulation indicators and gallstones: a cross-sectional study based on NHANES 2017–2020

BackgroundObesity is a major contributing factor to the formation of gallstones. As early identification typically results in improved outcomes, we explored the relationship between visceral lipid accumulation indicators and the occurrence of gallstones.MethodsThis cross-sectional study involved 3,224 adults. The researchers employed multivariable logistic regression, smoothed curve fitting (SCF), threshold effects analysis, and subgroup analysis to examine the relationship between metabolic scores for visceral fat (METS-VF), waist circumference (WC), lipid accumulation products (LAP), and visceral adiposity index (VAI) and gallstones. A Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis was used to identify key factors which were then used in the construction of a nomogram model. The diagnostic efficacy of this model in detecting gallstones was then determined using receiver operating characteristic curves.ResultsVisceral lipid accumulation indicators were strongly linked to the likelihood of having gallstones. Specific saturation effects for METS-VF, WC, LAP, and VAI and gallstones were determined using SCF. The inflection points for these effects were found to be 8.565, 108.400, 18.056, and 1.071, respectively. Subgroup analyses showed that associations remained consistent in most subgroups. The nomogram model, which was developed using critical features identified by LASSO regression, demonstrated excellent discriminatory ability, as indicated by an area under the curve value of 0.725.ConclusionsStudies have shown that increases in METS-VF, WC, LAP, and VAI are linked to increased prevalences of gallstones. The nomogram model, designed with critical parameters identified using LASSO regression, exhibits a strong association with the presence of gallstones.

Construction of mitochondrial quality regulation genes-related prognostic model based on bulk-RNA-seq analysis in multiple myeloma.

Mitochondrial quality regulation plays an important role in affecting the treatment sensitivity of multiple myeloma (MM). We aimed to develop a mitochondrial quality regulation genes (MQRGs)-related prognostic model for MM patients. The Genomic Data Commons-MM of bulk RNA-seq, mutation, and single-cell RNA-seq (scRNA-seq) dataset were downloaded, and the MQRGs gene set was collected previous study. "maftools" and CIBERSORT were used for mutation and immune-infiltration analysis. Subsequently, the "ConsensusClusterPlus" was used to perform the unsupervised clustering analysis, "survminer" and "ssGSEA" R package was used for the Kaplan-Meier survival and enrichment analysis, "limma" R, univariate and Least Absolute Shrinkage and Selection Operator Cox were used for RiskScore model. The "timeROC" R package was used for Receiver Operating Characteristic Curve analysis. Finally, the "Seurat" R package was used for scRNA-seq analysis. These MQRGs are mainly located on chromosome-1,2,3,7, and 22 and had significant expression differences among age, gender, and stage groups, in which PPARGC1A and PPARG are the high mutation genes. Most MQRGs expression are closely associated with the plasma cells infiltration and can divide the patients into 2 different prognostic clusters (C1, C2). Then, 8 risk models were screened from 60 DEGs for RiskScore, which is an independent prognostic factor and effectively divided the patients into high and low risk groups with significant difference of immune checkpoint expression. Nomogram containing RiskScore can accurately predict patient prognosis, and a series of specific transcription factor PRDM1 and IRF1 were identified. We described the based molecular features and developed a high effective MQRGs-related prognostic model in MM.

An Approach for Combining Clinical Judgment with Machine Learning to Inform Medical Decision Making: Analysis of Nonemergency Surgery Strategies for Acute Appendicitis in Patients with Multiple Long-Term Conditions.

Machine learning (ML) methods can identify complex patterns of treatment effect heterogeneity. However, before ML can help to personalize decision making, transparent approaches must be developed that draw on clinical judgment. We develop an approach that combines clinical judgment with ML to generate appropriate comparative effectiveness evidence for informing decision making. We motivate this approach in evaluating the effectiveness of nonemergency surgery (NES) strategies, such as antibiotic therapy, for people with acute appendicitis who have multiple long-term conditions (MLTCs) compared with emergency surgery (ES). Our 4-stage approach 1) draws on clinical judgment about which patient characteristics and morbidities modify the relative effectiveness of NES; 2) selects additional covariates from a high-dimensional covariate space (P > 500) by applying an ML approach, least absolute shrinkage and selection operator (LASSO), to large-scale administrative data (N = 24,312); 3) generates estimates of comparative effectiveness for relevant subgroups; and 4) presents evidence in a suitable form for decision making. This approach provides useful evidence for clinically relevant subgroups. We found that overall NES strategies led to increases in the mean number of days alive and out-of-hospital compared with ES, but estimates differed across subgroups, ranging from 21.2 (95% confidence interval: 1.8 to 40.5) for patients with chronic heart failure and chronic kidney disease to -10.4 (-29.8 to 9.1) for patients with cancer and hypertension. Our interactive tool for visualizing ML output allows for findings to be customized according to the specific needs of the clinical decision maker. This principled approach of combining clinical judgment with an ML approach can improve trust, relevance, and usefulness of the evidence generated for clinical decision making. Machine learning (ML) methods have many potential applications in medical decision making, but the lack of model interpretability and usability constitutes an important barrier for the wider adoption of ML evidence in practice.We develop a 4-stage approach for integrating clinical judgment into the way an ML approach is used to estimate and report comparative effectiveness.We illustrate the approach in undertaking an evaluation of nonemergency surgery (NES) strategies for acute appendicitis in patients with multiple long-term conditions and find that NES strategies lead to better outcomes compared with emergency surgery and that the effects differ across subgroups.We develop an interactive tool for visualizing the results of this study that allows findings to be customized according to the user's preferences.

Data-Driven Prognostication in Distal Medium Vessel Occlusions Using Explainable Machine Learning.

Distal medium vessel occlusions (DMVOs) are estimated to cause acute ischemic stroke (AIS) in 25-40% of cases. Prognostic models can inform patient counseling and research by enabling outcome predictions. However, models designed specifically for DMVOs are lacking. This retrospective study developed a machine learning model to predict 90-day unfavorable outcome [defined as a modified Rankin Scale (mRS) score of 3-6] in 164 primary DMVO patients. A model developed with the TabPFN algorithm utilized selected clinical, laboratory, imaging, and treatment data with the Least Absolute Shrinkage and Selection Operator feature selection. Performance was evaluated via 5-repeat 5-fold cross-validation. Model discrimination and calibration were evaluated. SHapley Additive Explanations (SHAP) identified influential features. A web application deployed the model for individualized predictions. The model achieved an area under the receiver operating characteristic curve of 0.815 (95% CI: 0.79-0.841) for predicting unfavorable outcome, demonstrating good discrimination, and a Brier score of 0.19 (95% CI: 0.177-0.202), demonstrating good calibration. SHAP analysis ranked admission National Institutes of Health Stroke Scale (NIHSS) score, premorbid mRS, type of thrombectomy, modified thrombolysis in cerebral infarction score, and history of malignancy as top predictors. The web application enables individualized prognostication. Our machine learning model demonstrated good discrimination and calibration for predicting 90-day unfavorable outcomes in primary DMVO strokes. This study demonstrates the potential for personalized prognostic counseling and research to support precision medicine in stroke care and recovery. ABC = definition; XYZ = definition. DMVO = Distal medium vessel occlusion; AIS = acute ischemic stroke; mRS = modified Rankin Scale; SHAP = SHapley Additive Explanations; NIHSS = National Institutes of Health Stroke Scale; ST = stroke thrombectomy; TRIPOD = Transparent Reporting of Multivariable Prediction Models for Individual Prognosis or Diagnosis; CT = computed tomography; CTP = CT perfusion; MRI = magnetic resonance imaging; CTA = CT angiography; DVT = deep vein thrombosis; PE = pulmonary emboli; TIA = transient ischemic attack; BMI = body mass index; ALP = alkaline phosphatase; ALT = alanine transaminase; AST = aspartate aminotransferase; NCCT-ASPECTS = Alberta Stroke Program Early CT Score; IVT = intravenous thrombolysis; mTICI = modified thrombolysis in cerebral infarction; ER = emergency room; kNN = k-nearest neighbor; LASSO = Least Absolute Shrinkage and Selection Operator; PDPs = partial dependence plots; ROC = receiver operating characteristic; PRC = precision-recall curve; AUROC = area under the ROC curve; AUPRC = area under the PRC; CI = confidence interval.

Development of Predictive Statistical Model for Gaining Valuable Insights in Pharmaceutical Product Recalls.

The rapid progress in artificial intelligence (AI) has revolutionized problem-solving across various domains. The global challenge of pharmaceutical product recalls imposes the development of effective tools to control and reduce shortage of pharmaceutical products and help avoid such recalls. This study employs AI, specifically machine learning (MI), to analyze critical factors influencing formulation, manufacturing, and formulation complexity which could offer promising avenue for optimizing drug development processes. Utilizing FDAZilla and SafeRX tools, an open database model was constructed, and predictive statistical models were developed using Multivariate Analysis and the Least Absolute Shrinkage and Selection Operator (LASSO) Approach. The study focuses on key descriptors such as delivery route, dosage form, dose, BCS classification, solid-state and physicochemical properties, release type, half-life, and manufacturing complexity. Through statistical analysis, a data simplification process identifies critical descriptors, assigning risk numbers and computing a cumulative risk number to assess product complexity and recall likelihood. Partial Least Square Regression and the LASSO approach established quantitative relationships between key descriptors and cumulative risk numbers. Results have identified key descriptors; BCS Class I, dose number, release profile, and drug half-life influencing product recall risk. The LASSO model further confirms these identified descriptors with 71% accuracy. In conclusion, the study presents a holistic AI and machine learning approach for evaluating and forecasting pharmaceutical product recalls, underscoring the importance of descriptors, formulation complexity, and manufacturing processes in mitigating risks associated with product quality.

Machine Learning Assisted Stroke Prediction in Mechanical Circulatory Support: Predictive Role of Systemic Mitochondrial Dysfunction.

Stroke continues to be a major adverse event in advanced congestive heart failure (CHF) patients after continuous-flow left ventricular assist device (CF-LVAD) implantation. Abnormalities in mitochondrial oxidative phosphorylation (OxPhos) have been critically implicated in the pathogenesis of neurodegenerative diseases and cerebral ischemia. We hypothesize that prior stroke may be associated with systemic mitochondrial OxPhos abnormalities, and impaired more in post-CF-LVAD patients with risk of developing new stroke. We studied 50 CF-LVAD patients (25 with prior stroke, 25 without); OxPhos complex proteins (complex I [C.I]-complex V [C.V]) were measured in blood leukocytes. Both at baseline (pre-CF-LVAD) and postoperatively (post-CF-LVAD), the prior-stroke group had significantly lower C.I, complex II (C.II), complex IV (C.IV), and C.V proteins when compared to the no-prior-stroke group. Oxidative phosphorylation proteins were significantly decreased in prior-stroke group at post-CF-LVAD compared to pre-CF-LVAD. Machine learning Least Absolute Shrinkage and Selection Operator (LASSO) and Random Forest modeling identified six prognostic factors that predicted postoperative stroke with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.93. Oxidative phosphorylation protein reduction appeared to be associated with the new stroke after implantation. Our study found for the first time the existence of mitochondrial dysfunction at the peripheral level in CHF patients with prior ischemic stroke even before CF-LVAD implantation. The changes in OxPhos protein expression could serve as biomarkers in predicting new post-CF-LVAD strokes.

Clustering-aided prediction of outcomes in patients with idiopathic pulmonary fibrosis

BackgroundBlood biomarkers predictive of the progression of idiopathic pulmonary fibrosis (IPF) would be of value for research and clinical practice. We used data from the IPF-PRO Registry to investigate whether the addition of “omics” data to risk prediction models based on demographic and clinical characteristics improved prediction of the progression of IPF.MethodsThe IPF-PRO Registry enrolled patients with IPF at 46 sites across the US. Patients were followed prospectively. Median follow-up was 27.2 months. Prediction models for disease progression included omics data (proteins and microRNAs [miRNAs]), demographic factors and clinical factors, all assessed at enrollment. Data on proteins and miRNAs were included in the models either as raw values or based on clusters in various combinations. Least absolute shrinkage and selection operator (Lasso) Cox regression was applied for time-to-event composite outcomes and logistic regression with L1 penalty was applied for binary outcomes assessed at 1 year. Model performance was assessed using Harrell’s C-index (for time-to-event outcomes) or area under the curve (for binary outcomes).ResultsData were analyzed from 231 patients. The models based on demographic and clinical factors, with or without omics data, were the top-performing models for prediction of all the time-to-event outcomes. Relative changes in average C-index after incorporating omics data into models based on demographic and clinical factors ranged from 1.7 to 3.2%. Of the blood biomarkers, surfactant protein-D, serine protease inhibitor A7 and matrix metalloproteinase-9 (MMP-9) were among the top predictors of the outcomes. For the binary outcomes, models based on demographics alone and models based on demographics plus omics data had similar performances. Of the blood biomarkers, CC motif chemokine 11, vascular cell adhesion protein-1, adiponectin, carcinoembryonic antigen and MMP-9 were the most important predictors of the binary outcomes.ConclusionsWe identified circulating protein and miRNA biomarkers associated with the progression of IPF. However, the integration of omics data into prediction models that included demographic and clinical factors did not materially improve the performance of the models.Trial registrationClinicalTrials.gov; No: NCT01915511; registered August 5, 2013; URL: www.clinicaltrials.gov.

Prognosis prediction of head and neck squamous cell carcinoma through the basement membrane-related lncRNA risk model

BackgroundHead and neck squamous cell carcinoma (HNSCC) ranks among the most widespread and significantly heterogeneous malignant tumors globally. Increasing evidence suggests that the basement membrane (BM) and associated long non-coding RNAs (lncRNA) are correlated with the onset of HNSCC and its prognosis. Our study aims to construct a basement membrane-associated lncRNAs (BMlncRNAs) marker to accurately predict the prognosis of HNSCC patients and find novel immunotherapy targets.MethodsThe Cancer Genome Atlas (TCGA) database was accessed to acquire the transcriptome expression matrices, somatic mutation data, and clinical follow-up data of HNSCC patients. Utilizing co-expression analysis, the BMlncRNAs were identified and the differentially expressed lncRNAs (DEBMlncRNA) were then filtered, The filtering thresholds are FDR&amp;lt;0.05 and |log2FC|≥1. Furthermore, univariate analysis, least absolute shrinkage and selection operator (LASSO), and multivariable Cox regression were utilized to develop the risk model. The model then underwent thorough evaluation across diverse perspectives, encompassing tumor immune infiltration, tumor mutation burden (TMB), functional enrichment, and chemotherapy sensitivity.ResultsThe risk assessment model consists of 14 BMlncRNA pairs. The acquired data is indicative of the reliability of the risk score in its capacity as a prognostic factor. Individuals at high risk exhibited a poorer prognosis, and a statistically significant variance was noted in TMB and tumor immune infiltration compared to the low-risk group. Additionally, heightened sensitivity to paclitaxel and docetaxel was evident in the patients at high risk.ConclusionWe have established a BMLncRNA-based prognostic model that can provide clinical guidance for future laboratory and clinical studies of HNSCC.

Deciphering the role of lipid metabolism-related genes in Alzheimer’s disease: a machine learning approach integrating Traditional Chinese Medicine

BackgroundAlzheimer’s disease (AD) represents a progressive neurodegenerative disorder characterized by the accumulation of misfolded amyloid beta protein, leading to the formation of amyloid plaques and the aggregation of tau protein into neurofibrillary tangles within the cerebral cortex. The role of carbohydrates, particularly apolipoprotein E (ApoE), is pivotal in AD pathogenesis due to its involvement in lipid and cholesterol metabolism, and its status as a genetic predisposition factor for the disease. Despite its significance, the mechanistic contributions of Lipid Metabolism-related Genes (LMGs) to AD remain inadequately elucidated. This research endeavor seeks to bridge this gap by pinpointing biomarkers indicative of early-stage AD, with an emphasis on those linked to immune cell infiltration. To this end, advanced machine-learning algorithms and data derived from the Gene Expression Omnibus (GEO) database have been employed to facilitate the identification of these biomarkers.MethodsDifferentially expressed genes (DEGs) were identified by comparing gene expression profiles between healthy individuals and Alzheimer’s disease (AD) patients, using data from two Gene Expression Omnibus (GEO) datasets: GSE5281 and GSE138260. Functional enrichment analysis was conducted to elucidate the biological relevance of the DEGs. To ensure the reliability of the results, samples were randomly divided into training and validation sets. The analysis focused on lipid metabolism-related DEGs (LMDEGs) to explore potential biomarkers for AD. Machine learning algorithms, including Support Vector Machine-Recursive Feature Elimination (SVM-RFE) and the Least Absolute Shrinkage and Selection Operator (LASSO) regression model, were applied to identify a key gene biomarker. Additionally, immune cell infiltration and its relationship with the gene biomarker were assessed using the CIBERSORT algorithm. The Integrated Traditional Chinese Medicine (ITCM) database was also referenced to identify Chinese medicines related to lipid metabolism and their possible connection to AD. This comprehensive strategy aims to integrate modern computational methods with traditional medicine to deepen our understanding of AD and its underlying mechanisms.ResultsThe study identified 137 genes from a pool of 751 lipid metabolism-related genes (LMGs) significantly associated with autophagy and immune response mechanisms. Through the application of LASSO and SVM-RFE machine-learning techniques, four genes—choline acetyl transferase (CHAT), member RAS oncogene family (RAB4A), acyl-CoA binding domain-containing protein 6 (ACBD6), and alpha-galactosidase A (GLA)—emerged as potential biomarkers for Alzheimer’s disease (AD). These genes demonstrated strong therapeutic potential due to their involvement in critical biological pathways. Notably, nine Chinese medicine compounds were identified to target these marker genes, offering a novel treatment approach for AD. Further, ceRNA network analysis revealed complex regulatory interactions involving these genes, underscoring their importance in AD pathology. CIBERSORT analysis highlighted a potential link between changes in the immune microenvironment and CHAT expression levels in AD patients, providing new insights into the immunological dimensions of the disease.ConclusionThe discovery of these gene markers offers substantial promise for the diagnosis and understanding of Alzheimer’s disease (AD). However, further investigation is necessary to validate their clinical utility. This study illuminates the role of Lipid Metabolism-related Genes (LMGs) in AD pathogenesis, offering potential targets for therapeutic intervention. It enhances our grasp of AD’s complex mechanisms and paves the way for future research aimed at refining diagnostic and treatment strategies.

Evaluating Maize Residue Cover Using Machine Learning and Remote Sensing in the Meadow Soil Region of Northeast China

The management of crop residues in farmland is crucial for increasing soil organic matter and reducing soil erosion. Identifying the regional extent of crop residue cover (CRC) is vital for implementing conservation tillage and formulating agricultural subsidy policies. The Google Earth Engine (GEE) and remote sensing images from 2019 to 2023 were used to obtain spectral characteristics before the maize seedling stage in Northeast China, followed by constructing the CRC estimation models using machine learning algorithms. To avoid the impact of multicollinearity among data, three machine learning algorithms—ridge regression (RR), partial least squares regression (PLSR), and least absolute shrinkage and selection operator (LASSO)—were employed. By comparing the accuracy of these methods, the most accurate model was determined and applied to subsequent CRC estimation. Based on the estimated CRC and Conservation Technology Information Center definitions of tillage practices, the conservation tillage mapping was completed, and the spatiotemporal distribution characteristics were thoroughly analyzed. The following findings were demonstrated: (1) the PLSR-based model outperformed RR (Pearson’s correlation coefficient (r) = 0.8875, R2 = 0.7877, RMSE = 6.99%) and LASSO (r = 0.8903, R2 = 0.7926, RMSE = 6.88%) with higher accuracy (r = 0.9264, R2 = 0.8582, RMSE = 4.93%). (2) Over the five years, the average no-tillage (NT) proportion in the study area was 15.9%, reduced tillage (RT) was 17.8%, and conventional tillage (CT) was 66.3%. In 2020 and 2022, NT rates were significantly higher at 27.5% and 15.5%, while RT were 15.7% and 30.0%, respectively. (3) Compared to the Sanjiang and Liaohe Plains (RT = 1907 km2 and 1336 km2, and NT = 559 km2 and 585 km2, respectively), the Songnen Plain exhibited higher conservation tillage rates (where RT was 3791 km2 and NT was 1265 km2). This provides crucial scientific evidence for the management and planning of conservation tillage, thereby optimizing farmland production planning, enhancing production efficiency, and promoting the development of sustainable agricultural production systems.

Comparison in prostate cancer diagnosis with PSA 4–10 ng/mL: radiomics-based model VS. PI-RADS v2.1

BackgroundTo evaluate accuracy of MRI-based radiomics in diagnosing prostate cancer (PCa) in patients with PSA levels between 4 and 10 ng/mL and compare it with the latest Prostate Imaging Reporting and Data System (PI-RADS v2.1) score.Methods221 patients with prostate lesions and PSA levels in 4–10 ng/mL, including 154 and 67 cases in the training and validation groups. Pathological confirmation of all patients was accomplished by the use of MRI-TRUS fusion targeted biopsy or systematic transrectal ultrasound (TRUS) guided biopsy. 851 radiomic features were extracted from each lesion of ADC and T2WI images. The least absolute shrinkage and selection operator (LASSO) regression algorithm and logistic regression were employed to select features and build the ADC and T2WI model. The combined model was obtained based on the ADC and T2WI features. The clinical benefit and diagnostic accuracy of the three radiomics models and PI-RADS v2.1 score were evaluated.Results10 radiomic features were ultimately selected from the ADC images, 13 from the T2WI images and 7 from the combined models. The ADC, T2WI and combined models achieved satisfactory diagnostic accuracy in the training [AUC:0.945 (ADC), 0.939 (T2WI), 0.979 (combined)] and validation groups [AUC: 0.942 (ADC), 0.943 (T2WI), 0.959 (combined)], which was significantly higher than those in PI-RADS v2.1 model (0.825 for training cohort and 0.853 for validation cohort). Compared with the PI-RADS v2.1 score, the three radiomics models generated superior PCa diagnostic performance in both the training (p = 0.002, p = 0.005, p < 0.001) and validation groups (p = 0.045, p = 0.035, p = 0.015).ConclusionRadiomics based on ADC and T2WI images can better identify PCa in patients with PSA 4–10 ng/mL, and MRI-based radiomics significantly outperforms the PI-RADS v2.1 score.Clinical trial numberNot applicable.

Expression Profile and Prognostic Significance of Pivotal Regulators for N7-Methylguanosine Methylation in Diffuse Large B-Cell Lymphoma.

N7-methylguanosine (m7G) occurs by adding a methyl group to the N7 atom of the RNA guanine. Emerging evidence suggests that m7G modification has emerged as a crucial regulator of tumorigenesis, progression, invasion, and metastasis in multiple cancers. Nevertheless, the utility of m7G modification in diffuse large B-cell lymphoma (DLBCL) remains undefined, notably the interaction with the tumor microenvironment (TME). Here, we aimed to identify the expression profile of m7G regulators in DLBCL, construct a novel risk model, and explore their connection with TME. We initially investigated the difference and correlation in m7G regulators' expression in normal and tumor groups, classified patients by consistent clustering analysis, investigated the functional and prognostic significance of the resulting subtypes, and identified prognosis-associated genes by one-way Cox and least absolute shrinkage and selection operator (LASSO)regression calculations, and constructed a risk model. Further analysis showed that correlation among immune cell infiltration with m7G risk score and determined that it impacts the prognosis of DLBCL patients. Our research demonstrated the relevance of m7G regulators to DLBCL prognosis, providing theoretical support for precise prognostic stratification and immunotherapeutic assessment in DLBCL.

Analysis of risk factors for painful diabetic peripheral neuropathy and construction of a prediction model based on Lasso regression

ObjectiveTo evaluate the prevalence and risk factors of painful diabetic peripheral neuropathy (PDPN) in patients with type 2 diabetic peripheral neuropathy (DPN) in Hunan Province, and establish and verify the prediction model.MethodsThis was a retrospective study involving 4908 patients, all patients were randomly divided into the training dataset(3436 cases)and the validation dataset (1472 cases) in a ratio of 7:3. Electroneurogram, clinical signs,and symptoms were used to evaluate neuropathy. Least absolute shrinkage and selection operator (LASSO) regression was used to select the optimal factors, and multifactorial logistic regression analysis was used to build a clinical prediction model. Calibration plots, decision curve analysis (DCA), and subject work characteristic curves (ROC) were used to assess the predictive effects.ResultThe prevalence of PDPN was 33.2%, and the multivariate logistic regression model showed that peripheral artery disease, duration of diabetes, smoking, and HBA1c were independent risk factors for PDPN in patients with type 2 diabetes. ROC analysis results showed that the AUC of the established prediction model was 0.872 in the training dataset and 0.843 in the validation dataset. The calibration curve and decision curve show that the model has good consistency and significant net benefit.Conclusion33.2% of DPN patients had PDPN in Hunan Province, China. Peripheral artery disease, duration of diabetes, smoking, and HBA1c are risk factors for PDPN in patients with type 2 diabetes. The prediction model is based on the above factors, which can well predict the probability of PDPN.

Ustekinumab affects myofibroblast metabolism to alleviate intestinal fibrosis by targeting KDELC1 in Crohn’s disease through multi-machine learning combined with single-cell sequencing analysis

BackgroundUstekinumab (UST), a biologic against interleukin (IL)-12/23, is commonly used to treat Crohn’s disease (CD). Myofibroblast (MF) is known as one of the most important factors causing intestinal fibrosis, and UST has been reported to alleviate this condition. However, the genetic mechanisms underlying UST’s effects on CD remain unclear. This study uses bioinformatics tools to analyze the genes and potential pathways affected by UST in CD, with a focus on its anti-fibrosis effects, providing insights into new therapeutic targets.MethodsThe data downloaded from the Gene Expression Omnibus (GEO) database were analyzed to screen for differentially expressed genes (DEGs). Various machine learning strategies, including the least absolute shrinkage and selection operator (LASSO), support vector machine (SVM), and random forest (RF), were employed to screen for key genes among the DEGs. Functional and pathway enrichment analyses were conducted, and key genes associated with myofibroblast (MF) activity were screened. Finally, endoscopic surgical specimens from CD patients and healthy participants were collected to assess the expression levels of collagen and key genes in intestinal tissues using hematoxylin–eosin (H&amp;amp;E), Masson staining, and immunohistochemistry.ResultsA total of 1,341 DEGs associated with CD were identified. Among them, 738 genes showed low expression in healthy populations but high expression in patients with CD, reduced expression after the treatment of UST. In contrast, 603 genes exhibited high expression in healthy individuals, showed low expression in CD patients, and increased expression after UST treatment. Functional and pathway analysis showed that DEGs were mainly concentrated in response to foreign biological stimuli and bacterial-derived molecules. DEGs are mainly enriched in chemokines, TNF, IL-17, and other signaling pathways. Seven key genes were identified: NCRNA00236, LOC730101, ORP3, XG, UBFD1, KDELC1, and RBP7. Single-cell analysis revealed that KDELC1 was closely related to MF activity. MFs with high KDELC1 expression were significantly enriched in biological functions, signaling pathways, and metabolic processes that promote fibrosis. The experiment showed that UST treatment helped maintain the integrity of intestinal tissue structure, reducing the expression levels of collagen I, KDELC1, and the severity of intestinal fibrosis. The functional and pathway analysis reiterated that DEGs were largely focused on responses to foreign biological stimuli and bacterial-derived molecules, as well as signaling pathways such as chemokines, TNF, and IL-17. Of the identified genes, KDELC1 showed a particularly strong correlation with MF activity in single-cell analysis (R = 0.33, p = 3.2e-07). MFs with high KDELC1 expression were closely linked to pathways promoting fibrosis progression, including TGF-β, epithelial-mesenchymal transformation, TNF/NF-κB, and related metabolic pathways such as vitamin B6 and arginine.ConclusionKDELC1 plays a key role in regulating multiple biological functions, including signaling pathways related to MF. UST alleviates intestinal fibrosis by targeting KDELC1, thereby influencing intramuscular fat metabolism and intercellular communication.

Development of Two Methods for Estimating High-Dimensional Data in the Case of Multicollinearity and Outliers

High-dimensional problems involve datasets or models characterized by a substantial number of variables or parameters prevalent across various domains such as statistics, machine learning, optimization, physics, and engineering. Challenges in these scenarios include computational complexity, data sparsity, over-fitting, and the curse of dimensionality. This study introduces two innovative techniques that combine the Random Forest machine learning approach with both the least absolute shrinkage and selection operator and the elastic net, which are statistical methodologies tailored to address high-dimensional challenges. We compared performance evaluations of these hybrid methods against traditional statistical approaches and standalone machine learning methods. The assessment is conducted using goodness-of-fit measures and involves both Monte Carlo simulation and a real-world application. The findings show that the strategies proposed in this study exhibit superior performance compared to conventional approaches when tackling high-dimensional challenges.