<b>OptimalCutpoints</b>: An<i>R</i>Package for Selecting Optimal Cutpoints in Diagnostic Tests

López-Ratón, Mónica; Rodríguez‐Álvarez, María Xosé; Cadarso‐Suárez, Carmen; Gude‐Sampedro, Francisco

doi:10.18637/jss.v061.i08

Cited by 495 publications

(407 citation statements)

References 69 publications

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“…13,19,22,23 In the present study, multiple regression analysis disclosed a relation between preoperative MMSE, cognitive change after ELD, and the outcome after shunt therapy. Patients with an MMSE below 21 and/ or worsening of cognitive function after ELD should be regarded as high risk for nonresponse to shunt therapy, especially when ROut measurements show pathological values above the cutoff of 14 mm Hg/ml/min.…”

Section: Discussionsupporting

confidence: 58%

Idiopathic normal pressure hydrocephalus: diagnostic and predictive value of clinical testing, lumbar drainage, and CSF dynamics

Mahr¹,

Dengl²,

Nestler³

et al. 2016

JNS

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591CliNiCal artiCle J Neurosurg 125:591-597, 2016 I dIopathIc normal pressure hydrocephalus (iNPH) has been a challenging entity for the past 50 years, since its first description by Hakim.21 Despite extensive research, its pathophysiological basis and pathogenesis remain matters of ongoing debate. Due to the uncertainty in diagnostic measures, several algorithms, diagnostic tools, and scoring systems have been proposed. A recent multicenter trial based the decision for surgical therapy on clinical signs and symptoms only, dividing cases into questionable and typical iNPH.23 Given the multitude of noninvasive and invasive measures to select symptomatic patients for hydrocephalus therapy, a prospective analysis of diagnostic and predictive parameters and their individual contributions within the diagnostic algorithm was warranted. Patients and MethodsPatients with suspicious clinical and MRI signs for iNPH were examined in a prospective study. Local ethics committee approval was obtained.abbreviatioNs AMP Q = ICP amplitude quotient; ELD = external lumbar drainage; ETV = endoscopic third ventriculostomy; ICP = intracranial pressure; iNPH = idiopathic normal pressure hydrocephalus; LIFT = lumbar infusion test; MMSE = Mini-Mental State Examination; mRS = modified Rankin Scale; OVM = overnight ICP monitoring; RAP = correlation coefficient between pulse amplitude and ICP; ROC = receiver operating characteristic; ROut = resistance to outflow of CSF; SLHS = Stein and Langfitt Hydrocephalus Score; VP = ventriculoperitoneal; ∆Kiefer = change in Kiefer score. obJeCtive The aim of the study was to analyze the diagnostic and predictive values of clinical tests, CSF dynamics, and intracranial pulsatility tests, compared with external lumbar drainage (ELD), for shunt response in patients with idiopathic normal pressure hydrocephalus (iNPH). Methods Sixty-eight consecutive patients with suspected iNPH were prospectively evaluated. Preoperative assessment included clinical tests, overnight intracranial pressure (ICP) monitoring, lumbar infusion test (LIFT), and ELD for 24-72 hours. Simple and multiple linear regression analyses were conducted to identify predictive parameters concerning the outcome after shunt therapy. results Positive response to ELD correctly predicted improvement after CSF diversion in 87.9% of the patients. A Mini-Mental State Examination (MMSE) value below 21 was associated with nonresponse after shunt insertion (specificity 93%, sensitivity 67%). Resistance to outflow of CSF (ROut) > 12 mm Hg/ml/min was false negative in 21% of patients. Intracranial pulsatility parameters yielded different results in various parameters (correlation coefficient between pulse amplitude and ICP, slow wave amplitude, and mean ICP) but did not correlate to outcome. In multiple linear regression analysis, a calculation of presurgical MMSE versus the value after ELD, ROut, and ICP amplitude quotient during LIFT was significantly associated with outcome (p = 0.04). CoNClusioNs Despite a multitude of invasive tests, presurgical cl...

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Section: Discussionsupporting

confidence: 58%

Idiopathic normal pressure hydrocephalus: diagnostic and predictive value of clinical testing, lumbar drainage, and CSF dynamics

Mahr¹,

Dengl²,

Nestler³

et al. 2016

JNS

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“…The linear mixed models were fitted with the R package "lme4" (72). The R package "OpticalCutpoints" was used to determine the cutoff point of the indirect ELISA and the derived estimates of the sensitivity and specificity with a 95% confidence interval (CI) (73). Accession number(s).…”

Section: Methodsmentioning

confidence: 99%

Postepizootic Persistence of Asymptomatic Mycoplasma conjunctivae Infection in Iberian Ibex

Fernández-Aguilar

Cabezón

Granados

et al. 2017

Appl Environ Microbiol

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The susceptibility of the Iberian ibex (Capra pyrenaica) to Mycoplasma conjunctivae ocular infection and the changes in their interaction over time were studied in terms of clinical outcome, molecular detection, and IgG immune response in a captive population that underwent a severe infectious keratoconjunctivitis (IKC) outbreak. Mycoplasma conjunctivae was detected in the Iberian ibex, coinciding with the IKC outbreak. Its prevalence had a decreasing trend in 2013 that was consistent with the clinical resolution (August, 35.4%; September, 8.7%; November, 4.3%). Infections without clinical outcome were, however, still detected in the last handling in November. Sequencing and cluster analyses of the M. conjunctivae strains found 1 year later in the ibex population confirmed the persistence of the same strain lineage that caused the IKC outbreak but with a high prevalence (75.3%) of mostly asymptomatic infections and with lower DNA load of M. conjunctivae in the eyes (mean quantitative PCR [qPCR] cycle threshold [C T ], 36.1 versus 20.3 in severe IKC). Significant age-related differences of M. conjunctivae prevalence were observed only under IKC epizootic conditions. No substantial effect of systemic IgG on M. conjunctivae DNA in the eye was evidenced with a linear mixed-models selection, which indicated that systemic IgG does not necessarily drive the resolution of M. conjunctivae infection and does not explain the epidemiological changes observed. The results show how both epidemiological scenarios, i.e., severe IKC outbreak and mostly asymptomatic infections, can consecutively occur by entailing mycoplasma persistence.IMPORTANCE Mycoplasma infections are reported in a wide range of epidemiological scenarios that involve severe disease to asymptomatic infections. This study allows a better understanding of the transition between two different Mycoplasma conjunctivae epidemiological scenarios described in wild host populations and highlights the ability of M. conjunctivae to adapt, persist, and establish diverse interactions with its hosts. The proportion of asymptomatic and clinical M. conjunctivae infections in a host population may not be regarded only in response to intrinsic host species traits (i.e., susceptibility) but also to a specific host-pathogen interaction, which in turn influences the infection dynamics. Both epidemic infectious keratoconjunctivitis and a high prevalence of asymptomatic M. conjunctivae infections may occur in the same host population, depending on the circulation of M. conjunctivae, its maintenance, and the progression of the host-pathogen interactions.

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“…The four quantities often of interest in classification problems are: sensitivity (in this case, the percentage of correctly identified remitters from the entire population of remitters), specificity (the percentage of correctly identified nonremitters from the entire population of nonremitters), positive predictive value (the percentage of predicted remitters who are truly remitters), and negative predictive value (the percentage of predicted nonremitters who are truly nonremitters). Assuming a high certainty (minimum of 70%) to accurately identify participants likely to be a remitter -that is, when you predict someone to be a remitter you will be correct 70% of the time -the optimal probability threshold as identified by the OptimalCutpoints package in R will make correct predictions 73.3% of the time and with 23.4% sensitivity [54]. Such a threshold might be desirable for a clinician, who would hope to be quite confident in the likelihood of placebo response before making a treatment decision for his/her patients.…”

Section: Prediction Of Placebo Outcomesmentioning

confidence: 99%

A Novel Strategy to Identify Placebo Responders: Prediction Index of Clinical and Biological Markers in the EMBARC Trial

Trivedi

South

Rush³

et al. 2018

Psychother Psychosom

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Background: One in three clinical trial patients with major depressive disorder report symptomatic improvement with placebo. Strategies to mitigate the effect of placebo responses have focused on modifying study design with variable success. Identifying and excluding or controlling for individuals with a high likelihood of responding to placebo may improve clinical trial efficiency and avoid unnecessary medication trials. Methods: Participants included those assigned to the placebo arm (n = 141) of the Establishing Moderators and Biosignatures for Antidepressant Response in Clinical Care (EMBARC) trial. The elastic net was used to evaluate 283 baseline clinical, behavioral, imaging, and electrophysiological variables to identify the most robust yet parsimonious features that predicted depression severity at the end of the double-blind 8-week trial. Variables retained in at least 50% of the 100 imputed data sets were used in a Bayesian multiple linear regression model to simultaneously predict the probabilities of response and remission. Results: Lower baseline depression severity, younger age, absence of melancholic features or history of physical abuse, less anxious arousal, less anhedonia, less neuroticism, and higher average theta current density in the rostral anterior cingulate predicted a higher likelihood of improvement with placebo. The Bayesian model predicted remission and response with an actionable degree of accuracy (both AUC > 0.73). An interactive calculator was developed predicting the likelihood of placebo response at the individual level. Conclusion: Easy-to-measure clinical, behavioral, and electrophysiological assessments can be used to identify placebo responders with a high degree of accuracy. Development of this calculator based on these findings can be used to identify potential placebo responders.

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OptimalCutpoints: AnRPackage for Selecting Optimal Cutpoints in Diagnostic Tests

Cited by 495 publications

References 69 publications

Idiopathic normal pressure hydrocephalus: diagnostic and predictive value of clinical testing, lumbar drainage, and CSF dynamics

Idiopathic normal pressure hydrocephalus: diagnostic and predictive value of clinical testing, lumbar drainage, and CSF dynamics

Postepizootic Persistence of Asymptomatic Mycoplasma conjunctivae Infection in Iberian Ibex

A Novel Strategy to Identify Placebo Responders: Prediction Index of Clinical and Biological Markers in the EMBARC Trial

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