Triage Modeling for Differential Diagnosis Between COVID-19 and Human Influenza A Pneumonia: Classification and Regression Tree Analysis.
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ABSTRACT:
SUBMITTER: Xiao A
PROVIDER: S-EPMC8382719 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Praziquantel (PZQ) is an effective chemotherapy for schistosomiasis mansoni and a mainstay for its control and potential elimination. However, it does not prevent against reinfection, which can occur rapidly in areas with active transmission. A guide to ranking the risk factors for Schistosoma mansoni reinfection would greatly contribute to prioritizing resources and focusing prevention and control measures to prevent rapid reinfection. The objective of the current study was to explore the relationship among the socioeconomic, demographic, and epidemiological factors that can influence reinfection by S. mansoni one year after successful treatment with PZQ in school-aged children in Northeastern Minas Gerais state Brazil. Parasitological, socioeconomic, demographic, and water contact information were surveyed in 506 S. mansoni-infected individuals, aged 6 to 15 years, resident in these endemic areas. Eligible individuals were treated with PZQ until they were determined to be negative by the absence of S. mansoni eggs in the feces on two consecutive days of Kato-Katz fecal thick smear. These individuals were surveyed again 12 months from the date of successful treatment with PZQ. A classification and regression tree modeling (CART) was then used to explore the relationship between socioeconomic, demographic, and epidemiological variables and their reinfection status. The most important risk factor identified for S. mansoni reinfection was their "heavy" infection at baseline. Additional analyses, excluding heavy infection status, showed that lower socioeconomic status and a lower level of education of the household head were also most important risk factors for S. mansoni reinfection. Our results provide an important contribution toward the control and possible elimination of schistosomiasis by identifying three major risk factors that can be used for targeted treatment and monitoring of reinfection. We suggest that control measures that target heavily infected children in the most economically disadvantaged households would be most beneficial to maintain the success of mass chemotherapy campaigns.
| S-EPMC5558968 | biostudies-literature
Project description:BACKGROUND:In the typical setting of gene-selection problems from high-dimensional data, e.g., gene expression data from microarray or next-generation sequencing-based technologies, an enormous volume of high-throughput data is generated, and there is often a need for a simple, computationally-inexpensive, non-parametric screening procedure than can quickly and accurately find a low-dimensional variable subset that preserves biological information from the original very high-dimensional data (dimension p > 40,000). This is in contrast to the very sophisticated variable selection methods that are computationally expensive, need pre-processing routines, and often require calibration of priors. RESULTS:We present a tree-based sequential CART (S-CART) approach to variable selection in the binary classification setting and compare it against the more sophisticated procedures using simulated and real biological data. In simulated data, we analyze S-CART performance versus (i) a random forest (RF), (ii) a fully-parametric Bayesian stochastic search variable selection (SSVS), and (iii) the moderated t-test statistic from the LIMMA package in R. The simulation study is based on a hierarchical Bayesian model, where dataset dimensionality, percentage of significant variables, and substructure via dependency vary. Selection efficacy is measured through false-discovery and missed-discovery rates. In all scenarios, the S-CART method is seen to consistently outperform SSVS and RF in both speed and detection accuracy. We demonstrate the utility of the S-CART technique both on simulated data and in a control-treatment mouse study. We show that the network analysis based on the S-CART-selected gene subset in essence recapitulates the biological findings of the study using only a fraction of the original set of genes considered in the study's analysis. CONCLUSIONS:The relatively simple-minded gene selection algorithms like S-CART may often in practical circumstances be preferred over much more sophisticated ones. The advantage of the "greedy" selection methods utilized by S-CART and the likes is that they scale well with the problem size and require virtually no tuning or training while remaining efficient in extracting the relevant information from microarray-like datasets containing large number of redundant or irrelevant variables. AVAILABILITY:The MATLAB 7.4b code for the S-CART implementation is available for download from https://neyman.mcg.edu/posts/scart.zip.
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Project description:Background:Pneumonia complicated by septic shock is associated with significant morbidity and mortality. Classification and regression tree methodology is an intuitive method for predicting clinical outcomes using binary splits. We aimed to improve the prediction of in-hospital mortality in patients with pneumonia and septic shock using decision tree analysis. Methods:Classification and regression tree models were applied to all patients with pneumonia-associated septic shock in the international, multicenter Cooperative Antimicrobial Therapy of Septic Shock database between 1996 and 2015. The association between clinical factors (time to appropriate antimicrobial therapy, severity of illness) and in-hospital mortality was evaluated. Accuracy in predicting clinical outcomes, sensitivity, specificity, and area under receiver operating curve of the final model was evaluated in training (n?=?2111) and testing datasets (n?=?2111). Results:The study cohort contained 4222 patients, and in-hospital mortality was 51%. The mean time from onset of shock to administration of appropriate antimicrobials was significantly higher for patients who died (17.2 h) compared to those who survived (5.0 h). In the training dataset (n?=?2111), a tree model using Acute Physiology and Chronic Health Evaluation II Score, lactate, age, and time to appropriate antimicrobial therapy yielded accuracy of 73% and area under the receiver operating curve 0.75. The testing dataset (n?=?2111) had accuracy of 69% and area under the receiver operating curve 0.72. Conclusions:Overall mortality (51%) in patients with pneumonia complicated by septic shock is high. Increased time to administration of antimicrobial therapy, Acute Physiology and Chronic Health Evaluation II Score, serum lactate, and age were associated with increased in-hospital mortality. Classification and regression tree methodology offers a simple prognostic model with good performance in predicting in-hospital mortality.
| S-EPMC6186142 | biostudies-literature
Project description:INTRODUCTION:The COVID-19 pandemic occurred amid the cancer immunotherapy revolution. Immune checkpoint inhibitors (ICIs) have become the standard of care for several solid cancers and are associated with peculiar toxicities, including pneumonitis which has similar features to COVID-19 pneumonia. AREAS COVERED:We summarize the main hallmarks of lung injury induced by ICIs and severe acute respiratory syndrome coronavirus 2 and discuss the critical aspects for differential diagnosis and management. Symptoms and radiological findings are often similar; conversely, treatments are quite different. Furthermore, we focus on potential interactions generating hypotheses that need confirmatory studies. EXPERT OPINION:All cancer patients treated with immunotherapy should receive screening for SARS-CoV-2. This would improve the diagnosis and management of pneumonia and guide therapeutic choices. Furthermore, clinicians could estimate the risk/benefit of continuing ICI treatment in COVID-19 positive patients. Temporary withdrawal of the immunotherapy treatment pending resolution of viral infection may be a reasonable option in long-responders patients.
| S-EPMC7441753 | biostudies-literature
Project description:BackgroundDiabetes in childhood and adolescence includes autoimmune and non-autoimmune forms with heterogeneity in clinical and biochemical presentations. An unresolved question is whether there are subtypes, endotypes, or theratypes within these forms of diabetes.MethodsThe multivariable classification and regression tree (CART) analysis method was used to identify subgroups of diabetes with differing residual C-peptide levels in patients with newly diagnosed diabetes before 20 years of age (n=1192). The robustness of the model was assessed in a confirmation and prognosis cohort (n=2722).FindingsThe analysis selected age, haemoglobin A1c (HbA1c), and body mass index (BMI) as split parameters that classified patients into seven islet autoantibody-positive and three autoantibody-negative groups. There were substantial differences in genetics, inflammatory markers, diabetes family history, lipids, 25-OH-Vitamin D3, insulin treatment, insulin sensitivity and insulin autoimmunity among the groups, and the method stratified patients with potentially different pathogeneses and prognoses. Interferon-ɣ and/or tumour necrosis factor inflammatory signatures were enriched in the youngest islet autoantibody-positive groups and in patients with the lowest C-peptide values, while higher BMI and type 2 diabetes characteristics were found in older patients. The prognostic relevance was demonstrated by persistent differences in HbA1c at 7 years median follow-up.InterpretationThis multivariable analysis revealed subgroups of young patients with diabetes that have potential pathogenetic and therapeutic relevance.FundingThe work was supported by funds from the German Federal Ministry of Education and Research (01KX1818; FKZ 01GI0805; DZD e.V.), the Innovative Medicine Initiative 2 Joint Undertaking INNODIA (grant agreement No. 115797), the German Robert Koch Institute, and the German Diabetes Association.
| S-EPMC9270253 | biostudies-literature
Project description:Dentine hypersensitivity (DH) affects people's quality of life (QoL). However changes in the internal meaning of QoL, known as Response shift (RS) may undermine longitudinal assessment of QoL. This study aimed to describe patterns of RS in people with DH using Classification and Regression Trees (CRT) and to explore the convergent validity of CRT with the then-test and ideals approaches.Data from an 8-week clinical trial of mouthwashes for dentine hypersensitivity (n = 75) using the Dentine Hypersensitivity Experience Questionnaire (DHEQ) as the outcome measure, were analysed. CRT was used to examine 8-week changes in DHEQ total score as a dependent variable with clinical status for DH and each DHEQ subscale score (restrictions, coping, social, emotional and identity) as independent variables. Recalibration was inferred when the clinical change was not consistent with the DHEQ change score using a minimally important difference for DHEQ of 22 points. Reprioritization was inferred by changes in the relative importance of each subscale to the model over time.Overall, 50.7% of participants experienced a clinical improvement in their DH after treatment and 22.7% experienced an important improvement in their quality of life. Thirty-six per cent shifted their internal standards downward and 14.7% upwards, suggesting recalibration. Reprioritization occurred over time among the social and emotional impacts of DH.CRT was a useful method to reveal both, the types and nature of RS in people with a mild health condition and demonstrated convergent validity with design based approaches to detect RS.
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Project description:In this research, the photoplethysmogram (PPG) waveform analysis is utilized to develop a logistic regression-based predictive model for the classification of diabetes. The classifier has three predictors age, b/a, and SP indices in which they achieved an overall accuracy of 92.3% in the prediction of diabetes. In this study, a total of 587 subjects were enrolled. A total of 459 subjects were used for model training and development, while the rest of the 128 subjects were used for model testing and validation. The classifier was able to diagnose 63 patients correctly as diabetes while 27 subjects were wrongly classified as nondiabetes with an accuracy of 70%. Again, the model classified 479 subjects as nondiabetes correctly while it incorrectly classified 18 subjects as diabetes with an accuracy of 96.4%. Finally, the proposed model revealed an overall predictive accuracy of 92.3% which makes it a reliable surrogate measure for diabetes classification and prediction in clinical settings.
| S-EPMC7439205 | biostudies-literature
Project description:BACKGROUND:There is a need for shorter-length assessments that capture patient questionnaire data while attaining high data quality without an undue response burden on patients. Computerized adaptive testing (CAT) and classification and regression tree (CART) methods have the potential to meet these needs and can offer attractive options to shorten questionnaire lengths. OBJECTIVE:The objective of this study was to test whether CAT or CART was best suited to reduce the number of questionnaire items in multiple domains (eg, anxiety, depression, quality of life, and social support) used for a needs assessment procedure (NAP) within the field of cardiac rehabilitation (CR) without the loss of data quality. METHODS:NAP data of 2837 CR patients from a multicenter Cardiac Rehabilitation Decision Support System (CARDSS) Web-based program was used. Patients used a Web-based portal, MyCARDSS, to provide their data. CAT and CART were assessed based on their performances in shortening the NAP procedure and in terms of sensitivity and specificity. RESULTS:With CAT and CART, an overall reduction of 36% and 72% of NAP questionnaire length, respectively, was achieved, with a mean sensitivity and specificity of 0.765 and 0.817 for CAT, 0.777 and 0.877 for classification trees, and 0.743 and 0.40 for regression trees, respectively. CONCLUSIONS:Both CAT and CART can be used to shorten the questionnaires of the NAP used within the field of CR. CART, however, showed the best performance, with a twice as large overall decrease in the number of questionnaire items of the NAP compared to CAT and the highest sensitivity and specificity. To our knowledge, our study is the first to assess the differences in performance between CAT and CART for shortening questionnaire lengths. Future research should consider administering varied assessments of patients over time to monitor their progress in multiple domains. For CR professionals, CART integrated with MyCARDSS would provide a feedback loop that informs the rehabilitation progress of their patients by providing real-time patient measurements.
| S-EPMC7055848 | biostudies-literature
Project description:PurposeRisk factors for obesity and weight gain are typically evaluated individually while "adjusting for" the influence of other confounding factors, and few studies, if any, have created risk profiles by clustering risk factors. We identified subgroups of postmenopausal women homogeneous in their clustered modifiable and non-modifiable risk factors for gaining ? 3% weight.MethodsThis study included 612 postmenopausal women 50-79 years old, enrolled in an ancillary study of the Women's Health Initiative Observational Study between February 1995 and July 1998. Classification and regression tree and stepwise regression models were built and compared.ResultsOf 27 selected variables, the factors significantly related to ? 3% weight gain were weight change in the past 2 years, age at menopause, dietary fiber, fat, alcohol intake, and smoking. In women younger than 65 years, less than 4 kg weight change in the past 2 years sufficiently reduced risk of ? 3% weight gain. Different combinations of risk factors related to weight gain were reported for subgroups of women: women 65 years or older (essential factor: < 9.8 g/day dietary factor), African Americans (essential factor: currently smoking), and white women (essential factor: ? 5 kg weight change for the past 2 years).ConclusionsOur findings suggest specific characteristics for particular subgroups of postmenopausal women that may be useful for identifying those at risk for weight gain. The study results may be useful for targeting efforts to promote strategies to reduce the risk of obesity and weight gain in subgroups of postmenopausal women and maximize the effect of weight control by decreasing obesity-relevant adverse health outcomes.
| S-EPMC4378852 | biostudies-literature
Project description:BackgroundBoth hyperkalemia and hypokalemia can lead to cardiac arrhythmias and are associated with increased mortality. Information on the predictors of potassium in individuals with diabetes in routine clinical practice is lacking.ObjectiveTo identify predictors of hyperkalemia and hypokalemia in adults with diabetes.DesignRetrospective cohort study, with classification and regression tree (CART) analysis.Participants321,856 individuals with diabetes enrolled in four large integrated health care systems from 2012 to 2013.Main measuresWe used a single serum potassium result collected in 2012 or 2013. Hyperkalemia was defined as a serum potassium ≥ 5.5 mEq/L and hypokalemia as < 3.5 mEq/L. Predictors included demographic factors, laboratory measurements, comorbidities, medication use, and health care utilization.Key resultsThere were 2556 hypokalemia events (0.8%) and 1517 hyperkalemia events (0.5%). In univariate analyses, we identified concordant predictors (associated with increased probability of both hyperkalemia and hypokalemia), discordant predictors, and predictors of only hyperkalemia or hypokalemia. In CART models, the hyperkalemia "tree" had 5 nodes and a c-statistic of 0.76. The nodes were defined by prior potassium results and eGFRs, and the 5 terminal "leaves" had hyperkalemia probabilities of 0.2 to 7.2%. The hypokalemia tree had 4 nodes and a c-statistic of 0.76. The hypokalemia tree included nodes defined by prior potassium results, and the 4 terminal leaves had hypokalemia probabilities of 0.3 to 17.6%. Individuals with a recent potassium between 4.0 and 5.0 mEq/L, eGFR ≥ 45 mL/min/1.73m2, and no hypokalemia in the previous year had a < 1% rate of either hypokalemia or hyperkalemia.ConclusionsThe yield of routine serum potassium testing may be low in individuals with a recent serum potassium between 4.0 and 5.0 mEq/L, eGFR ≥ 45 mL/min/1.73m2, and no recent history of hypokalemia. We did not examine the effect of recent changes in clinical condition or medications on acute potassium changes.
| S-EPMC7403274 | biostudies-literature