scholarly journals Development and prospective external validation of a tool to predict poor recovery at 9 months after acute ankle sprain in UK emergency departments: the SPRAINED prognostic model

BMJ Open ◽  
2018 ◽  
Vol 8 (11) ◽  
pp. e022802 ◽  
Author(s):  
Michael M Schlussel ◽  
David J Keene ◽  
Gary S Collins ◽  
Jennifer Bostock ◽  
Christopher Byrne ◽  
...  

ObjectivesTo develop and externally validate a prognostic model for poor recovery after ankle sprain.Setting and participantsModel development used secondary data analysis of 584 participants from a UK multicentre randomised clinical trial. External validation used data from 682 participants recruited in 10 UK emergency departments for a prospective observational cohort.Outcome and analysisPoor recovery was defined as presence of pain, functional difficulty or lack of confidence in the ankle at 9 months after injury. Twenty-three baseline candidate predictors were included together in a multivariable logistic regression model to identify the best predictors of poor recovery. Relationships between continuous variables and the outcome were modelled using fractional polynomials. Regression parameters were combined over 50 imputed data sets using Rubin’s rule. To minimise overfitting, regression coefficients were multiplied by a heuristic shrinkage factor and the intercept re-estimated. Incremental value of candidate predictors assessed at 4 weeks after injury was explored using decision curve analysis and the baseline model updated. The final models included predictors selected based on the Akaike information criterion (p<0.157). Model performance was assessed by calibration and discrimination.ResultsOutcome rate was lower in the development (6.7%) than in the external validation data set (19.9%). Mean age (29.9 and 33.6 years), body mass index (BMI; 26.3 and 27.1 kg/m2), pain when resting (37.8 and 38.5 points) or bearing weight on the ankle (75.4 and 71.3 points) were similar in both data sets. Age, BMI, pain when resting, pain bearing weight, ability to bear weight, days from injury until assessment and injury recurrence were the selected predictors. The baseline model had fair discriminatory ability (C-statistic 0.72; 95% CI 0.66 to 0.79) but poor calibration. The updated model presented better discrimination (C-statistic 0.78; 95% CI 0.72 to 0.84), but equivalent calibration.ConclusionsThe models include predictors easy to assess clinically and show benefit when compared with not using any model.Trial registration numberISRCTN12726986; Results.

2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Warren Mukelabai Simangolwa

Appropriate open defecation free (ODF) sustainability interventions are key to further mobilise communities to consume sanitation and hygiene products and services that enhance household’s quality of life and embed household behavioural change for heathier communities. This study aims to develop a logistic regression derived risk algorithm to estimate a 12-month ODF slippage risk and externally validate the model in an independent data set. ODF slippage occurs when one or more toilet adequacy parameters are no longer present for one or more toilets in a community. Data in the Zambia district health information software for water sanitation and hygiene management information system for Chungu and Chabula chiefdoms was used for the study. The data was retrieved from the date of chief Chungu and Chabula chiefdoms' attainment of ODF status in October 2016 for 12 months until September 2017 for the development and validation data sets respectively. Data was assumed to be missing completely at random and the complete case analysis approach was used. The events per variables were satisfactory for both the development and validation data sets. Multivariable regression with a backwards selection procedure was used to decide candidate predictor variables with p < 0.05 meriting inclusion. To correct for optimism, the study compared amount of heuristic shrinkage by comparing the model’s apparent C-statistic to the C- statistic computed by nonparametric bootstrap resampling. In the resulting model, an increase in the covariates ‘months after ODF attainment’, ‘village population’ and ‘latrine built after CLTS’, were all associated with a higher probability of ODF slippage. Conversely, an increase in the covariate ‘presence of a handwashing station with soap’, was associated with reduced probability of ODF slippage. The predictive performance of the model was improved by the heuristic shrinkage factor of 0.988. The external validation confirmed good prediction performance with an area under the receiver operating characteristic curve of 0.85 and no significant lack of fit (Hosmer-Lemeshow test: p = 0.246). The results must be interpreted with caution in regions where the ODF definitions, culture and other factors are different from those asserted in the study.


2011 ◽  
Vol 2011 ◽  
pp. 1-6 ◽  
Author(s):  
Takashi Imamoto ◽  
Takanobu Utsumi ◽  
Makoto Takano ◽  
Atsushi Komaru ◽  
Satoshi Fukasawa ◽  
...  

Objective. The aim of this study is to develop a prognostic model capable of predicting the probability of significant upgrading among Japanese patients.Methods. The study cohort comprised 508 men treated with RP, with available prostate-specific antigen levels, biopsy, and RP Gleason sum values. Clinical and pathological data from 258 patients were obtained from another Japanese institution for validation.Results. Significant Gleason sum upgrading was recorded in 92 patients (18.1%) at RP. The accuracy of the nomogram predicting the probability of significant Gleason sum upgrading between biopsy and RP specimens was 88.9%. Overall AUC was 0.872 when applied to the validation data set. Nomogram predictions of significant upgrading were within 7.5% of an ideal nomogram.Conclusions. Nearly one-fifth of Japanese patients with prostate cancer will be significantly upgraded. Our nomogram seems to provide considerably accurate predictions regardless of minor variations in pathological assessment when applied to Japanese patient populations.


Author(s):  
Zhiyi Wang ◽  
Jie Weng ◽  
Zhongwang Li ◽  
Ruonan Hou ◽  
Lebin Zhou ◽  
...  

BackgroundThe COVID-19 virus is an emerging virus rapidly spread worldwide This study aimed to establish an effective diagnostic nomogram for suspected COVID-19 pneumonia patients.METHODSWe used the LASSO aggression and multivariable logistic regression methods to explore the predictive factors associated with COVID-19 pneumonia, and established the diagnostic nomogram for COVID-19 pneumonia using multivariable regression. This diagnostic nomogram was assessed by the internal and external validation data set. Further, we plotted decision curves and clinical impact curve to evaluate the clinical usefulness of this diagnostic nomogram.RESULTSThe predictive factors including the epidemiological history, wedge- shaped or fan-shaped lesion parallel to or near the pleura, bilateral lower lobes, ground glass opacities, crazy paving pattern and white blood cell (WBC) count were contained in the nomogram. In the primary cohort, the C-statistic for predicting the probability of the COVID-19 pneumonia was 0.967, even higher than the C-statistic (0.961) in initial viral nucleic acid nomogram which was established using the univariable regression. The C-statistic was 0.848 in external validation cohort. Good calibration curves were observed for the prediction probability in the internal validation and external validation cohort. The nomogram both performed well in terms of discrimination and calibration. Moreover, decision curve and clinical impact curve were also beneficial for COVID- 19 pneumonia patients.CONCLUSIONOur nomogram can be used to predict COVID-19 pneumonia accurately and favourably.


2018 ◽  
Vol 22 (64) ◽  
pp. 1-112 ◽  
Author(s):  
David J Keene ◽  
Michael M Schlüssel ◽  
Jacqueline Thompson ◽  
Daryl A Hagan ◽  
Mark A Williams ◽  
...  

BackgroundAnkle sprains are very common injuries. Although recovery can occur within weeks, around one-third of patients have longer-term problems.ObjectivesTo develop and externally validate a prognostic model for identifying people at increased risk of poor outcome after an acute ankle sprain.DesignDevelopment of a prognostic model in a clinical trial cohort data set and external validation in a prospective cohort study.SettingEmergency departments (EDs) in the UK.ParticipantsAdults with an acute ankle sprain (within 7 days of injury).Sample sizeThere were 584 clinical trial participants in the development data set and 682 recruited for the external validation study.PredictorsCandidate predictor variables were chosen based on availability in the clinical data set, clinical consensus, face validity, a systematic review of the literature, data quality and plausibility of predictiveness of the outcomes.Main outcome measuresModels were developed to predict two composite outcomes representing poor outcome. Outcome 1 was the presence of at least one of the following symptoms at 9 months after injury: persistent pain, functional difficulty or lack of confidence. Outcome 2 included the same symptoms as outcome 1, with the addition of recurrence of injury. Rates of poor outcome in the external data set were lower than in the development data set, 7% versus 20% for outcome 1 and 16% versus 24% for outcome 2.AnalysisMultiple imputation was used to handle missing data. Logistic regression models, together with multivariable fractional polynomials, were used to select variables and identify transformations of continuous predictors that best predicted the outcome based on a nominal alpha of 0.157, chosen to minimise overfitting. Predictive accuracy was evaluated by assessing model discrimination (c-statistic) and calibration (flexible calibration plot).Results(1) Performance of the prognostic models in development data set – the combinedc-statistic for the outcome 1 model across the 50 imputed data sets was 0.74 [95% confidence interval (CI) 0.70 to 0.79], with good model calibration across the imputed data sets. The combinedc-statistic for the outcome 2 model across the 50 imputed data sets was 0.70 (95% CI 0.65 to 0.74), with good model calibration across the imputed data sets. Updating these models, which used baseline data collected at the ED, with an additional variable at 4 weeks post injury (pain when bearing weight on the ankle) improved the discriminatory ability (c-statistic 0.77, 95% CI 0.73 to 0.82, for outcome 1 and 0.75, 95% CI 0.71 to 0.80, for outcome 2) and calibration of both models. (2) Performance of the models in the external data set – the combinedc-statistic for the outcome 1 model across the 50 imputed data sets was 0.73 (95% CI 0.66 to 0.79), with a calibration plot intercept of –0.91 (95% CI –0.98 to 0.44) and slope of 1.13 (95% CI 0.76 to 1.50). The combinedc-statistic for the outcome 2 model across the 50 imputed data sets was 0.63 (95% CI 0.58 to 0.69), with a calibration plot intercept of –0.25 (95% CI –0.27 to 0.11) and slope of 1.03 (95% CI 0.65 to 1.42). The updated models with the additional pain variable at 4 weeks had improved discriminatory ability over the baseline models but not better calibration.ConclusionsThe SPRAINED (Synthesising a clinical Prognostic Rule for Ankle Injuries in the Emergency Department) prognostic models performed reasonably well, and showed benefit compared with not using any model; therefore, the models may assist clinical decision-making when managing and advising ankle sprain patients in the ED setting. The models use predictors that are simple to obtain.LimitationsThe data used were from a randomised controlled trial and so were not originally intended to fulfil the aim of developing prognostic models. However, the data set was the best available, including data on the symptoms and clinical events of interest.Future workFurther model refinement, including recalibration or identifying additional predictors, may be required. The effect of implementing and using either model in clinical practice, in terms of acceptability and uptake by clinicians and on patient outcomes, should be investigated.Trial registrationCurrent Controlled Trials ISRCTN12726986.FundingThis project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full inHealth Technology Assessment; Vol. 22, No. 64. See the NIHR Journals Library website for further project information. Funding was also recieved from the NIHR Collaboration for Leadership in Applied Health Research, Care Oxford at Oxford Health NHS Foundation Trust, NIHR Biomedical Research Centre, Oxford, and the NIHR Fellowship programme.


2020 ◽  
Author(s):  
Zhiyi Wang ◽  
Jie Weng ◽  
Zhongwang Li ◽  
Ruonan Hou ◽  
Lebin Zhou ◽  
...  

Abstract Background The COVID-19 virus is an emerging virus associated with severe respiratory illness first detected in December, 2019, and rapidly spread worldwide. The aim of this study was to establish an effective diagnostic nomogram for suspected COVID-19 pneumonia patients. Methods We used the LASSO aggression and multivariable logistic regression methods to explore the predictive factors associated with COVID-19 pneumonia, and established the diagnostic nomogram for COVID-19 pneumonia using multivariable regression. This diagnostic nomogram was assessed by the internal and external validation data set. Further, we plotted decision curves and clinical impact curve to evaluate the clinical usefulness of this diagnostic nomogram. Results The predictive factors including the epidemiological history, wedge-shaped or fan-shaped lesion parallel to or near the pleura, bilateral lower lobes, ground glass opacities, crazy paving pattern and white blood cell (WBC) count were contained in the nomogram. In the primary cohort, the C-statistic for predicting the probability of the COVID-19 pneumonia was 0.967, even higher than the C-statistic (0.961) in initial viral nucleic acid nomogram which was established using the univariable regression. The C-statistic was 0.848 in external validation cohort. Good calibration curves were observed for the prediction probability in the internal validation and external validation cohort. The nomogram both performed well in terms of discrimination and calibration. Moreover, decision curve and clinical impact curve were also beneficial for COVID-19 pneumonia patients. Conclusion Our nomogram can be used to predict COVID-19 pneumonia accurately and favourably.


BMJ Open ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. e040778
Author(s):  
Vineet Kumar Kamal ◽  
Ravindra Mohan Pandey ◽  
Deepak Agrawal

ObjectiveTo develop and validate a simple risk scores chart to estimate the probability of poor outcomes in patients with severe head injury (HI).DesignRetrospective.SettingLevel-1, government-funded trauma centre, India.ParticipantsPatients with severe HI admitted to the neurosurgery intensive care unit during 19 May 2010–31 December 2011 (n=946) for the model development and further, data from same centre with same inclusion criteria from 1 January 2012 to 31 July 2012 (n=284) for the external validation of the model.Outcome(s)In-hospital mortality and unfavourable outcome at 6 months.ResultsA total of 39.5% and 70.7% had in-hospital mortality and unfavourable outcome, respectively, in the development data set. The multivariable logistic regression analysis of routinely collected admission characteristics revealed that for in-hospital mortality, age (51–60, >60 years), motor score (1, 2, 4), pupillary reactivity (none), presence of hypotension, basal cistern effaced, traumatic subarachnoid haemorrhage/intraventricular haematoma and for unfavourable outcome, age (41–50, 51–60, >60 years), motor score (1–4), pupillary reactivity (none, one), unequal limb movement, presence of hypotension were the independent predictors as its 95% confidence interval (CI) of odds ratio (OR)_did not contain one. The discriminative ability (area under the receiver operating characteristic curve (95% CI)) of the score chart for in-hospital mortality and 6 months outcome was excellent in the development data set (0.890 (0.867 to 912) and 0.894 (0.869 to 0.918), respectively), internal validation data set using bootstrap resampling method (0.889 (0.867 to 909) and 0.893 (0.867 to 0.915), respectively) and external validation data set (0.871 (0.825 to 916) and 0.887 (0.842 to 0.932), respectively). Calibration showed good agreement between observed outcome rates and predicted risks in development and external validation data set (p>0.05).ConclusionFor clinical decision making, we can use of these score charts in predicting outcomes in new patients with severe HI in India and similar settings.


2019 ◽  
Author(s):  
Guangzhi Wang ◽  
Huihui Wan ◽  
Xingxing Jian ◽  
Yuyu Li ◽  
Jian Ouyang ◽  
...  

AbstractIn silico T-cell epitope prediction plays an important role in immunization experimental design and vaccine preparation. Currently, most epitope prediction research focuses on peptide processing and presentation, e.g. proteasomal cleavage, transporter associated with antigen processing (TAP) and major histocompatibility complex (MHC) combination. To date, however, the mechanism for immunogenicity of epitopes remains unclear. It is generally agreed upon that T-cell immunogenicity may be influenced by the foreignness, accessibility, molecular weight, molecular structure, molecular conformation, chemical properties and physical properties of target peptides to different degrees. In this work, we tried to combine these factors. Firstly, we collected significant experimental HLA-I T-cell immunogenic peptide data, as well as the potential immunogenic amino acid properties. Several characteristics were extracted, including amino acid physicochemical property of epitope sequence, peptide entropy, eluted ligand likelihood percentile rank (EL rank(%)) score and frequency score for immunogenic peptide. Subsequently, a random forest classifier for T cell immunogenic HLA-I presenting antigen epitopes and neoantigens was constructed. The classification results for the antigen epitopes outperformed the previous research (the optimal AUC=0.81, external validation data set AUC=0.77). As mutational epitopes generated by the coding region contain only the alterations of one or two amino acids, we assume that these characteristics might also be applied to the classification of the endogenic mutational neoepitopes also called ‘neoantigens’. Based on mutation information and sequence related amino acid characteristics, a prediction model of neoantigen was established as well (the optimal AUC=0.78). Further, an easy-to-use web-based tool ‘INeo-Epp’ was developed (available at http://www.biostatistics.online/INeo-Epp/neoantigen.php)for the prediction of human immunogenic antigen epitopes and neoantigen epitopes.


Author(s):  
André M. Carrington ◽  
Paul W. Fieguth ◽  
Hammad Qazi ◽  
Andreas Holzinger ◽  
Helen H. Chen ◽  
...  

Abstract Background In classification and diagnostic testing, the receiver-operator characteristic (ROC) plot and the area under the ROC curve (AUC) describe how an adjustable threshold causes changes in two types of error: false positives and false negatives. Only part of the ROC curve and AUC are informative however when they are used with imbalanced data. Hence, alternatives to the AUC have been proposed, such as the partial AUC and the area under the precision-recall curve. However, these alternatives cannot be as fully interpreted as the AUC, in part because they ignore some information about actual negatives. Methods We derive and propose a new concordant partial AUC and a new partial c statistic for ROC data—as foundational measures and methods to help understand and explain parts of the ROC plot and AUC. Our partial measures are continuous and discrete versions of the same measure, are derived from the AUC and c statistic respectively, are validated as equal to each other, and validated as equal in summation to whole measures where expected. Our partial measures are tested for validity on a classic ROC example from Fawcett, a variation thereof, and two real-life benchmark data sets in breast cancer: the Wisconsin and Ljubljana data sets. Interpretation of an example is then provided. Results Results show the expected equalities between our new partial measures and the existing whole measures. The example interpretation illustrates the need for our newly derived partial measures. Conclusions The concordant partial area under the ROC curve was proposed and unlike previous partial measure alternatives, it maintains the characteristics of the AUC. The first partial c statistic for ROC plots was also proposed as an unbiased interpretation for part of an ROC curve. The expected equalities among and between our newly derived partial measures and their existing full measure counterparts are confirmed. These measures may be used with any data set but this paper focuses on imbalanced data with low prevalence. Future work Future work with our proposed measures may: demonstrate their value for imbalanced data with high prevalence, compare them to other measures not based on areas; and combine them with other ROC measures and techniques.


2019 ◽  
Vol 7 (3) ◽  
pp. SE113-SE122 ◽  
Author(s):  
Yunzhi Shi ◽  
Xinming Wu ◽  
Sergey Fomel

Salt boundary interpretation is important for the understanding of salt tectonics and velocity model building for seismic migration. Conventional methods consist of computing salt attributes and extracting salt boundaries. We have formulated the problem as 3D image segmentation and evaluated an efficient approach based on deep convolutional neural networks (CNNs) with an encoder-decoder architecture. To train the model, we design a data generator that extracts randomly positioned subvolumes from large-scale 3D training data set followed by data augmentation, then feed a large number of subvolumes into the network while using salt/nonsalt binary labels generated by thresholding the velocity model as ground truth labels. We test the model on validation data sets and compare the blind test predictions with the ground truth. Our results indicate that our method is capable of automatically capturing subtle salt features from the 3D seismic image with less or no need for manual input. We further test the model on a field example to indicate the generalization of this deep CNN method across different data sets.


2016 ◽  
Vol 34 (2_suppl) ◽  
pp. 180-180
Author(s):  
Fang Liz Zhou ◽  
Justin Guinney ◽  
Tao Wang ◽  
J. Christopher Bare ◽  
Thea C Norman ◽  
...  

180 Background: Project Data Sphere, LLC (PDS) and Sage Bionetworks/DREAM have completed the “Prostate Cancer DREAM Challenge” (Challenge), a crowdsourced competition, using historical prostate cancer clinical trial data from PDS. The Challenge aimed to improve prognostic models for overall survival (OS) and to explore predictive models for treatment toxicity in mCRPC patients. Methods: Control arms of 4 randomized phase III trials (total 2,070 patients) were used as training and validation data sets for the Challenge: ASCENT2, MAINSAIL, VENICE and ENTHUSE33. All subjects were first line mCRPC patients receiving docetaxel treatment. Curated baseline clinical covariates (demographics, comorbidity, prior treatment, laboratory, lesion and vital signs) were modeled along with raw clinical data tables. The primary purpose of the Challenge was to develop a prognostic model for OS (SubChallenge 1). The models were scored using concordance index and integrated area under receiver operator curve (iAUC) from 6-30 months. The published mCRPC OS model of Halabi, et al., JCO, 2014, was used as the benchmark. Results: The Challenge attracted over 160 active participants who formed 50 teams that submitted final models for SubChallenge 1. Median iAUC was 0.76 (0.67-0.78) with a maximum score of 0.792. Over half (n = 35) of these models exceeded the published benchmark (0.743 iAUC). Teams explored new methodologies such as model-based imputation and machine learning techniques to develop the best performing models. Many leveraged raw clinical data sets to create their own covariates and expanded beyond existing prognostic models. Conclusions: The Challenge externally validated Halabi’s first line prognostic model. New prognostic models were proposed and validated with significant improvements over the benchmark. Further analyses are needed to examine the winning models for new prognostic factors and to validate them using additional trial data from PDS. The Challenge drove interest from cross-disciplinary teams of global experts to explore and enhance their technical abilities using real clinical data whilst serving as a vehicle to accelerate medical innovation.


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