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JCO Clinical Cancer Informatics Jun 2024The estimation of prognosis and life expectancy is critical in the care of patients with advanced cancer. To aid clinical decision making, we build a prognostic strategy...
PURPOSE
The estimation of prognosis and life expectancy is critical in the care of patients with advanced cancer. To aid clinical decision making, we build a prognostic strategy combining a machine learning (ML) model with explainable artificial intelligence to predict 1-year survival after palliative radiotherapy (RT) for bone metastasis.
MATERIALS AND METHODS
Data collected in the multicentric PRAIS trial were extracted for 574 eligible adults diagnosed with metastatic cancer. The primary end point was the overall survival (OS) at 1 year (1-year OS) after the start of RT. Candidate covariate predictors consisted of 13 clinical and tumor-related pre-RT patient characteristics, seven dosimetric and treatment-related variables, and 45 pre-RT laboratory variables. ML models were developed and internally validated using the Python package. The effectiveness of each model was evaluated in terms of discrimination. A Shapley Additive Explanations (SHAP) explainability analysis to infer the global and local feature importance and to understand the reasons for correct and misclassified predictions was performed.
RESULTS
The best-performing model for the classification of 1-year OS was the extreme gradient boosting algorithm, with AUC and F1-score values equal to 0.805 and 0.802, respectively. The SHAP technique revealed that higher chance of 1-year survival is associated with low values of interleukin-8, higher values of hemoglobin and lymphocyte count, and the nonuse of steroids.
CONCLUSION
An explainable ML approach can provide a reliable prediction of 1-year survival after RT in patients with advanced cancer. The implementation of SHAP analysis provides an intelligible explanation of individualized risk prediction, enabling oncologists to identify the best strategy for patient stratification and treatment selection.
Topics: Humans; Machine Learning; Bone Neoplasms; Palliative Care; Male; Female; Prognosis; Aged; Middle Aged; Algorithms
PubMed: 38917384
DOI: 10.1200/CCI.24.00027 -
Frontiers in Immunology 2024The identification of diagnostic and therapeutic biomarkers for Alzheimer's Disease (AD) remains a crucial area of research. In this study, utilizing the Weighted Gene...
The identification of diagnostic and therapeutic biomarkers for Alzheimer's Disease (AD) remains a crucial area of research. In this study, utilizing the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm, we identified RHBDF2 and TNFRSF10B as feature genes associated with AD pathogenesis. Analyzing data from the GSE33000 dataset, we revealed significant upregulation of RHBDF2 and TNFRSF10B in AD patients, with correlations to age and gender. Interestingly, their expression profile in AD differs notably from that of other neurodegenerative conditions. Functional analysis unveiled their involvement in immune response and various signaling pathways implicated in AD pathogenesis. Furthermore, our study demonstrated the potential of RHBDF2 and TNFRSF10B as diagnostic biomarkers, exhibiting high discrimination power in distinguishing AD from control samples. External validation across multiple datasets confirmed the robustness of the diagnostic model. Moreover, utilizing molecular docking analysis, we identified dinaciclib and tanespimycin as promising small molecule drugs targeting RHBDF2 and TNFRSF10B for potential AD treatment. Our findings highlight the diagnostic and therapeutic potential of RHBDF2 and TNFRSF10B in AD management, shedding light on novel strategies for precision medicine in AD.
Topics: Humans; Alzheimer Disease; Machine Learning; Biomarkers; Molecular Docking Simulation; Gene Regulatory Networks; Gene Expression Profiling; Transcriptome; Female; Male; Receptors, TNF-Related Apoptosis-Inducing Ligand
PubMed: 38915415
DOI: 10.3389/fimmu.2024.1333666 -
Neurobiology of Language (Cambridge,... 2024Reading is both a visual and a linguistic task, and as such it relies on both general-purpose, visual mechanisms and more abstract, meaning-oriented processes....
Reading is both a visual and a linguistic task, and as such it relies on both general-purpose, visual mechanisms and more abstract, meaning-oriented processes. Disentangling the roles of these resources is of paramount importance in reading research. The present study capitalizes on the coupling of fast periodic visual stimulation and MEG recordings to address this issue and investigate the role of different kinds of visual and linguistic units in the visual word identification system. We compared strings of pseudo-characters; strings of consonants (e.g., sfcl); readable, but unattested strings (e.g., amsi); frequent, but non-meaningful chunks (e.g., idge); suffixes (e.g., ment); and words (e.g., vibe); and looked for discrimination responses with a particular focus on the ventral, occipito-temporal regions. The results revealed sensitivity to alphabetic, readable, familiar, and lexical stimuli. Interestingly, there was no discrimination between suffixes and equally frequent, but meaningless endings, thus highlighting a lack of sensitivity to semantics. Taken together, the data suggest that the visual word identification system, at least in its early processing stages, is particularly tuned to form-based regularities, most likely reflecting its reliance on general-purpose, statistical learning mechanisms that are a core feature of the visual system as implemented in the ventral stream.
PubMed: 38911459
DOI: 10.1162/nol_a_00145 -
Nature Communications Jun 2024Metacognitive evaluations of confidence provide an estimate of decision accuracy that could guide learning in the absence of explicit feedback. We examine how humans...
Metacognitive evaluations of confidence provide an estimate of decision accuracy that could guide learning in the absence of explicit feedback. We examine how humans might learn from this implicit feedback in direct comparison with that of explicit feedback, using simultaneous EEG-fMRI. Participants performed a motion direction discrimination task where stimulus difficulty was increased to maintain performance, with intermixed explicit- and no-feedback trials. We isolate single-trial estimates of post-decision confidence using EEG decoding, and find these neural signatures re-emerge at the time of feedback together with separable signatures of explicit feedback. We identified these signatures of implicit versus explicit feedback along a dorsal-ventral gradient in the striatum, a finding uniquely enabled by an EEG-fMRI fusion. These two signals appear to integrate into an aggregate representation in the external globus pallidus, which could broadcast updates to improve cortical decision processing via the thalamus and insular cortex, irrespective of the source of feedback.
Topics: Humans; Decision Making; Male; Magnetic Resonance Imaging; Female; Adult; Basal Ganglia; Young Adult; Learning; Electroencephalography; Brain Mapping
PubMed: 38909014
DOI: 10.1038/s41467-024-49538-w -
The Lancet. Digital Health Jul 2024Pulmonary complications are the most common cause of death after surgery. This study aimed to derive and externally validate a novel prognostic model that can be used...
A prognostic model for use before elective surgery to estimate the risk of postoperative pulmonary complications (GSU-Pulmonary Score): a development and validation study in three international cohorts.
BACKGROUND
Pulmonary complications are the most common cause of death after surgery. This study aimed to derive and externally validate a novel prognostic model that can be used before elective surgery to estimate the risk of postoperative pulmonary complications and to support resource allocation and prioritisation during pandemic recovery.
METHODS
Data from an international, prospective cohort study were used to develop a novel prognostic risk model for pulmonary complications after elective surgery in adult patients (aged ≥18 years) across all operation and disease types. The primary outcome measure was postoperative pulmonary complications at 30 days after surgery, which was a composite of pneumonia, acute respiratory distress syndrome, and unexpected mechanical ventilation. Model development with candidate predictor variables was done in the GlobalSurg-CovidSurg Week dataset (global; October, 2020). Two structured machine learning techniques were explored (XGBoost and the least absolute shrinkage and selection operator [LASSO]), and the model with the best performance (GSU-Pulmonary Score) underwent internal validation using bootstrap resampling. The discrimination and calibration of the score were externally validated in two further prospective cohorts: CovidSurg-Cancer (worldwide; February to August, 2020, during the COVID-19 pandemic) and RECON (UK and Australasia; January to October, 2019, before the COVID-19 pandemic). The model was deployed as an online web application. The GlobalSurg-CovidSurg Week and CovidSurg-Cancer studies were registered with ClinicalTrials.gov, NCT04509986 and NCT04384926.
FINDINGS
Prognostic models were developed from 13 candidate predictor variables in data from 86 231 patients (1158 hospitals in 114 countries). External validation included 30 492 patients from CovidSurg-Cancer (726 hospitals in 75 countries) and 6789 from RECON (150 hospitals in three countries). The overall rates of pulmonary complications were 2·0% in derivation data, and 3·9% (CovidSurg-Cancer) and 4·7% (RECON) in the validation datasets. Penalised regression using LASSO had similar discrimination to XGBoost (area under the receiver operating curve [AUROC] 0·786, 95% CI 0·774-0·798 vs 0·785, 0·772-0·797), was more explainable, and required fewer covariables. The final GSU-Pulmonary Score included ten predictor variables and showed good discrimination and calibration upon internal validation (AUROC 0·773, 95% CI 0·751-0·795; Brier score 0·020, calibration in the large [CITL] 0·034, slope 0·954). The model performance was acceptable on external validation in CovidSurg-Cancer (AUROC 0·746, 95% CI 0·733-0·760; Brier score 0·036, CITL 0·109, slope 1·056), but with some miscalibration in RECON data (AUROC 0·716, 95% CI 0·689-0·744; Brier score 0·045, CITL 1·040, slope 1·009).
INTERPRETATION
This novel prognostic risk score uses simple predictor variables available at the time of a decision for elective surgery that can accurately stratify patients' risk of postoperative pulmonary complications, including during SARS-CoV-2 outbreaks. It could inform surgical consent, resource allocation, and hospital-level prioritisation as elective surgery is upscaled to address global backlogs.
FUNDING
National Institute for Health Research.
Topics: Humans; Elective Surgical Procedures; Postoperative Complications; Female; Prognosis; Middle Aged; Male; Prospective Studies; Aged; COVID-19; Risk Assessment; Adult; Machine Learning; Risk Factors; Lung Diseases; Cohort Studies
PubMed: 38906616
DOI: 10.1016/S2589-7500(24)00065-7 -
Annals of Medicine Dec 2024Patients with hip fractures frequently need to receive perioperative transfusions of concentrated red blood cells due to preoperative anemia or surgical blood loss....
BACKGROUND
Patients with hip fractures frequently need to receive perioperative transfusions of concentrated red blood cells due to preoperative anemia or surgical blood loss. However, the use of perioperative blood products increases the risk of adverse events, and the shortage of blood products is prompting us to minimize blood transfusion. Our study aimed to construct a machine learning algorithm predictive model to identify patients at high risk for perioperative transfusion early in hospital admission and to manage their patient blood to reduce transfusion requirements.
METHODS
This study collected patients hospitalized for hip fractures at a university hospital from May 2016 to November 2022. All patients included in the analysis were randomly divided into a training set and validation set according to 70:30. Eight machine learning algorithms, CART, GBM, KNN, LR, NNet, RF, SVM, and XGBoost, were used to construct the prediction models. The models were evaluated for discrimination, calibration, and clinical utility, and the best prediction model was selected.
RESULTS
A total of 805 patients were included in the study, of whom 306 received transfusions during the perioperative period. We screened eight features used to construct the prediction model: age, fracture time, fracture type, hemoglobin, albumin, creatinine, calcium ion, and activated partial thromboplastin time. After evaluating and comparing the performance of each of the eight models, the model constructed by the XGBoost algorithm had the best performance, with MCC values of 0.828 and 0.939 in the training and validation sets, respectively. In addition, it had good calibration and clinical utility in both the training and validation sets.
CONCLUSION
The model constructed by the XGBoost algorithm has the best performance, using this model to identify patients at high risk for transfusion early in their admission and promptly incorporating them into a patient blood management plan can help reduce the risk of transfusion.
Topics: Humans; Male; Hip Fractures; Aged; Machine Learning; Female; Blood Transfusion; Aged, 80 and over; Risk Assessment; Blood Loss, Surgical; Algorithms; Perioperative Care; Risk Factors
PubMed: 38902847
DOI: 10.1080/07853890.2024.2357225 -
Infection and Immunity Jun 2024Because most humans resist infection, there is a paucity of lung samples to study. To address this gap, we infected Diversity Outbred mice with and studied the lungs...
Because most humans resist infection, there is a paucity of lung samples to study. To address this gap, we infected Diversity Outbred mice with and studied the lungs of mice in different disease states. After a low-dose aerosol infection, progressors succumbed to acute, inflammatory lung disease within 60 days, while controllers maintained asymptomatic infection for at least 60 days, and then developed chronic pulmonary tuberculosis (TB) lasting months to more than 1 year. Here, we identified features of asymptomatic infection by applying computational and statistical approaches to multimodal data sets. Cytokines and anti-. cell wall antibodies discriminated progressors vs controllers with chronic pulmonary TB but could not classify mice with asymptomatic infection. However, a novel deep-learning neural network trained on lung granuloma images was able to accurately classify asymptomatically infected lungs vs acute pulmonary TB in progressors vs chronic pulmonary TB in controllers, and discrimination was based on perivascular and peribronchiolar lymphocytes. Because the discriminatory lesion was rich in lymphocytes and CD4 T cell-mediated immunity is required for resistance, we expected CD4 T-cell genes would be elevated in asymptomatic infection. However, the significantly different, highly expressed genes were from B-cell pathways (e.g., , , , , , , and ), and CD20+ B cells were enriched in the perivascular and peribronchiolar regions of mice with asymptomatic infection. Together, these results indicate that genetically controlled B-cell responses are important for establishing asymptomatic lung infection.
PubMed: 38899881
DOI: 10.1128/iai.00263-23 -
BMC Medical Informatics and Decision... Jun 2024Because spontaneous remission is common in IMN, and there are adverse effects of immunosuppressive therapy, it is important to assess the risk of progressive loss of...
BACKGROUND
Because spontaneous remission is common in IMN, and there are adverse effects of immunosuppressive therapy, it is important to assess the risk of progressive loss of renal function before deciding whether and when to initiate immunosuppressive therapy. Therefore, this study aimed to establish a risk prediction model to predict patient prognosis and treatment response to help clinicians evaluate patient prognosis and decide on the best treatment regimen.
METHODS
From September 2019 to December 2020, a total of 232 newly diagnosed IMN patients from three hospitals in Liaoning Province were enrolled. Logistic regression analysis selected the risk factors affecting the prognosis, and a dynamic online nomogram prognostic model was constructed based on extreme gradient boost, random forest, logistic regression machine learning algorithms. Receiver operating characteristic and calibration curves and decision curve analysis were utilized to assess the performance and clinical utility of the developed model.
RESULTS
A total of 130 patients were in the training cohort and 102 patients in the validation cohort. Logistic regression analysis identified four risk factors: course ≥ 6 months, UTP, D-dimer and sPLA2R-Ab. The random forest algorithm showed the best performance with the highest AUROC (0.869). The nomogram had excellent discrimination ability, calibration ability and clinical practicability in both the training cohort and the validation cohort.
CONCLUSIONS
The dynamic online nomogram model can effectively assess the prognosis and treatment response of IMN patients. This will help clinicians assess the patient's prognosis more accurately, communicate with the patient in advance, and jointly select the most appropriate treatment plan.
Topics: Humans; Nomograms; Female; Male; Middle Aged; Glomerulonephritis, Membranous; Adult; Prognosis; Risk Factors; Logistic Models
PubMed: 38898472
DOI: 10.1186/s12911-024-02568-2 -
Decoding electroencephalographic responses to visual stimuli compatible with electrical stimulation.APL Bioengineering Jun 2024Electrical stimulation of the visual nervous system could improve the quality of life of patients affected by acquired blindness by restoring some visual sensations, but...
Electrical stimulation of the visual nervous system could improve the quality of life of patients affected by acquired blindness by restoring some visual sensations, but requires careful optimization of stimulation parameters to produce useful perceptions. Neural correlates of elicited perceptions could be used for fast automatic optimization, with electroencephalography as a natural choice as it can be acquired non-invasively. Nonetheless, its low signal-to-noise ratio may hinder discrimination of similar visual patterns, preventing its use in the optimization of electrical stimulation. Our work investigates for the first time the discriminability of the electroencephalographic responses to visual stimuli compatible with electrical stimulation, employing a newly acquired dataset whose stimuli encompass the concurrent variation of several features, while neuroscience research tends to study the neural correlates of single visual features. We then performed above-chance single-trial decoding of multiple features of our newly crafted visual stimuli using relatively simple machine learning algorithms. A decoding scheme employing the information from multiple stimulus presentations was implemented, substantially improving our decoding performance, suggesting that such methods should be used systematically in future applications. The significance of the present work relies in the determination of which visual features can be decoded from electroencephalographic responses to electrical stimulation-compatible stimuli and at which granularity they can be discriminated. Our methods pave the way to using electroencephalographic correlates to optimize electrical stimulation parameters, thus increasing the effectiveness of current visual neuroprostheses.
PubMed: 38894958
DOI: 10.1063/5.0195680 -
Sensors (Basel, Switzerland) Jun 2024The potential of a voltametric E-tongue coupled with a custom data pre-processing stage to improve the performance of machine learning techniques for rapid...
The potential of a voltametric E-tongue coupled with a custom data pre-processing stage to improve the performance of machine learning techniques for rapid discrimination of tomato purées between cultivars of different economic value has been investigated. To this aim, a sensor array with screen-printed carbon electrodes modified with gold nanoparticles (GNP), copper nanoparticles (CNP) and bulk gold subsequently modified with poly(3,4-ethylenedioxythiophene) (PEDOT), was developed to acquire data to be transformed by a custom pre-processing pipeline and then processed by a set of commonly used classifiers. The GNP and CNP-modified electrodes, selected based on their sensitivity to soluble monosaccharides, demonstrated good ability in discriminating samples of different cultivars. Among the different data analysis methods tested, Linear Discriminant Analysis (LDA) proved to be particularly suitable, obtaining an average F1 score of 99.26%. The pre-processing stage was beneficial in reducing the number of input features, decreasing the computational cost, i.e., the number of computing operations to be performed, of the entire method and aiding future cost-efficient hardware implementation. These findings proved that coupling the multi-sensing platform featuring properly modified sensors with the custom pre-processing method developed and LDA provided an optimal tradeoff between analytical problem solving and reliable chemical information, as well as accuracy and computational complexity. These results can be preliminary to the design of hardware solutions that could be embedded into low-cost portable devices.
Topics: Solanum lycopersicum; Machine Learning; Gold; Discriminant Analysis; Electronic Nose; Metal Nanoparticles; Electrodes; Polymers; Copper; Bridged Bicyclo Compounds, Heterocyclic
PubMed: 38894376
DOI: 10.3390/s24113586