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  1. Article ; Online: Estimation in the progressive illness-death model: A nonexhaustive review.

    Meira-Machado, Luís / Sestelo, Marta

    Biometrical journal. Biometrische Zeitschrift

    2018  Volume 61, Issue 2, Page(s) 245–263

    Abstract: Multistate models can be successfully used for describing complex event history data, for example, describing stages in the disease progression of a patient. The so-called "illness-death" model plays a central role in the theory and practice of these ... ...

    Abstract Multistate models can be successfully used for describing complex event history data, for example, describing stages in the disease progression of a patient. The so-called "illness-death" model plays a central role in the theory and practice of these models. Many time-to-event datasets from medical studies with multiple end points can be reduced to this generic structure. In these models one important goal is the modeling of transition rates but biomedical researchers are also interested in reporting interpretable results in a simple and summarized manner. These include estimates of predictive probabilities, such as the transition probabilities, occupation probabilities, cumulative incidence functions, and the sojourn time distributions. We will give a review of some of the available methods for estimating such quantities in the progressive illness-death model conditionally (or not) on covariate measures. For some of these quantities estimators based on subsampling are employed. Subsampling, also referred to as landmarking, leads to small sample sizes and usually to heavily censored data leading to estimators with higher variability. To overcome this issue estimators based on a preliminary estimation (presmoothing) of the probability of censoring may be used. Among these, the presmoothed estimators for the cumulative incidences are new. We also introduce feasible estimation methods for the cumulative incidence function conditionally on covariate measures. The proposed methods are illustrated using real data. A comparative simulation study of several estimation approaches is performed and existing software in the form of R packages is discussed.
    MeSH term(s) Biostatistics/methods ; Disease Progression ; Humans ; Models, Statistical ; Mortality ; Software
    Language English
    Publishing date 2018-11-20
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 131640-0
    ISSN 1521-4036 ; 0323-3847 ; 0006-3452
    ISSN (online) 1521-4036
    ISSN 0323-3847 ; 0006-3452
    DOI 10.1002/bimj.201700200
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A method for determining groups in multiple survival curves.

    Villanueva, Nora M / Sestelo, Marta / Meira-Machado, Luís

    Statistics in medicine

    2018  Volume 38, Issue 5, Page(s) 866–877

    Abstract: Survival analysis includes a wide variety of methods for analyzing time-to-event data. One basic but important goal in survival analysis is the comparison of survival curves between groups. Several nonparametric methods have been proposed in the ... ...

    Abstract Survival analysis includes a wide variety of methods for analyzing time-to-event data. One basic but important goal in survival analysis is the comparison of survival curves between groups. Several nonparametric methods have been proposed in the literature to test for the equality of survival curves for censored data. When the null hypothesis of equality of curves is rejected, leading to the clear conclusion that at least one curve is different, it can be interesting to ascertain whether curves can be grouped or if all these curves are different from each other. A method is proposed that allows determining groups with an automatic selection of their number. The validity and behavior of the proposed method was evaluated through simulation studies. The applicability of the proposed method is illustrated using real data. Software in the form of an R package has been developed implementing the proposed method.
    MeSH term(s) Algorithms ; Colonic Neoplasms/mortality ; Computer Simulation ; Data Interpretation, Statistical ; Humans ; Kaplan-Meier Estimate ; Lung Neoplasms/mortality ; Models, Statistical ; Research Design/statistics & numerical data
    Language English
    Publishing date 2018-10-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 843037-8
    ISSN 1097-0258 ; 0277-6715
    ISSN (online) 1097-0258
    ISSN 0277-6715
    DOI 10.1002/sim.8016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Anxiety and/or depression: which symptoms contribute to adverse clinical outcomes after amputation?

    Pedras, Susana / Meira-Machado, Luís / Couto de Carvalho, André / Carvalho, Rui / Pereira, M Graça

    Journal of mental health (Abingdon, England)

    2020  Volume 31, Issue 6, Page(s) 792–800

    Abstract: Background: One of the most serious complications of diabetes mellitus (DM) is a diabetic foot ulcer (DFU), with lower extremity amputation (LEA).: Aims: This study aims to explore the role of anxiety and depression on mortality, reamputation and ... ...

    Abstract Background: One of the most serious complications of diabetes mellitus (DM) is a diabetic foot ulcer (DFU), with lower extremity amputation (LEA).
    Aims: This study aims to explore the role of anxiety and depression on mortality, reamputation and healing, after a LEA due to DFU.
    Methods: A sample of 149 patients with DFU who underwent LEA answered the Hospital Anxiety and Depression Scale and a sociodemographic and clinical questionnaire. This is a longitudinal and multicenter study with four assessment moments that used Cox proportional hazards models adjusted for demographic and clinical variables.
    Results: Rate of mortality, reamputation and healing, 10 months after LEA were 9.4%, 27.5% and 61.7%, respectively. Anxiety, at baseline, was negatively associated with healing. However, depression was not an independent predictor of mortality. None of the psychological factors was associated with reamputation.
    Conclusion: Results highlight the significant contribution of anxiety symptoms at pre-surgery, to healing after a LEA. Suggestions for psychological interventions are made.
    MeSH term(s) Humans ; Amputation, Surgical ; Diabetic Foot/surgery ; Anxiety ; Anxiety Disorders ; Risk Factors
    Language English
    Publishing date 2020-10-24
    Publishing country England
    Document type Multicenter Study ; Journal Article
    ZDB-ID 1145439-8
    ISSN 1360-0567 ; 0963-8237
    ISSN (online) 1360-0567
    ISSN 0963-8237
    DOI 10.1080/09638237.2020.1836554
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A Multistate Model for Analyzing Transitions Between Body Mass Index Categories During Childhood: The Generation XXI Birth Cohort Study.

    Moreira, Carla / Meira-Machado, Luís / Fonseca, Maria João / Santos, Ana Cristina

    American journal of epidemiology

    2018  Volume 188, Issue 2, Page(s) 305–313

    Abstract: Prevalences of overweight and obesity in young children have risen dramatically in the last several decades in most developed countries. Childhood overweight and obesity are known to have immediate and long-term health consequences and are now recognized ...

    Abstract Prevalences of overweight and obesity in young children have risen dramatically in the last several decades in most developed countries. Childhood overweight and obesity are known to have immediate and long-term health consequences and are now recognized as important public health concerns. We used a Markov 4-state model with states defined by 4 body mass index (BMI; weight (kg)/height (m)2) categories (underweight (<-2 standard deviations (SDs) of BMI z score), normal weight (-2 ≤ SD ≤ 1), overweight (1 < SD ≤ 2), and obese (>2 SDs of BMI z score)) to study the rates of transition to higher or lower BMI categories among children aged 4-10 years. We also used this model to study the relationships between explanatory variables and their transition rates. The participants consisted of 4,887 children from the Generation XXI Birth Cohort Study (Porto, Portugal; 2005-2017) who underwent anthropometric evaluation at age 4 years and in at least 1 of the subsequent follow-up waves (ages 7 and 10 years). Children who were normal weight were more likely to move to higher BMI categories than to lower categories, whereas overweight children had similar rates of transition to the 2 adjacent categories. We evaluated the associations of maternal age and education, type of delivery, sex, and birth weight with childhood overweight and obesity, but we observed statistically significant results only for sex and maternal education with regard to the progressive transitions.
    MeSH term(s) Anthropometry ; Birth Weight ; Body Mass Index ; Body-Weight Trajectory ; Child ; Child, Preschool ; Female ; Humans ; Male ; Markov Chains ; Pediatric Obesity/epidemiology ; Portugal/epidemiology ; Prevalence ; Sex Factors ; Socioeconomic Factors
    Language English
    Publishing date 2018-10-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2937-3
    ISSN 1476-6256 ; 0002-9262
    ISSN (online) 1476-6256
    ISSN 0002-9262
    DOI 10.1093/aje/kwy232
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Nonparametric estimation of the survival function for ordered multivariate failure time data: A comparative study.

    Meira-Machado, Luís / Sestelo, Marta / Gonçalves, Andreia

    Biometrical journal. Biometrische Zeitschrift

    2015  Volume 58, Issue 3, Page(s) 623–634

    Abstract: In longitudinal studies of disease, patients may experience several events through a follow-up period. In these studies, the sequentially ordered events are often of interest and lead to problems that have received much attention recently. Issues of ... ...

    Abstract In longitudinal studies of disease, patients may experience several events through a follow-up period. In these studies, the sequentially ordered events are often of interest and lead to problems that have received much attention recently. Issues of interest include the estimation of bivariate survival, marginal distributions, and the conditional distribution of gap times. In this work, we consider the estimation of the survival function conditional to a previous event. Different nonparametric approaches will be considered for estimating these quantities, all based on the Kaplan-Meier estimator of the survival function. We explore the finite sample behavior of the estimators through simulations. The different methods proposed in this article are applied to a dataset from a German Breast Cancer Study. The methods are used to obtain predictors for the conditional survival probabilities as well as to study the influence of recurrence in overall survival.
    MeSH term(s) Biometry/methods ; Breast Neoplasms/diagnosis ; Breast Neoplasms/epidemiology ; Female ; Germany/epidemiology ; Humans ; Models, Statistical ; Multivariate Analysis ; Probability ; Recurrence ; Statistics, Nonparametric ; Survival Analysis ; Time Factors
    Language English
    Publishing date 2015-10-12
    Publishing country Germany
    Document type Comparative Study ; Journal Article
    ZDB-ID 131640-0
    ISSN 1521-4036 ; 0323-3847 ; 0006-3452
    ISSN (online) 1521-4036
    ISSN 0323-3847 ; 0006-3452
    DOI 10.1002/bimj.201500038
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Nonparametric estimation of transition probabilities in the non-Markov illness-death model: A comparative study.

    de Uña-Álvarez, Jacobo / Meira-Machado, Luís

    Biometrics

    2015  Volume 71, Issue 2, Page(s) 364–375

    Abstract: Multi-state models are often used for modeling complex event history data. In these models the estimation of the transition probabilities is of particular interest, since they allow for long-term predictions of the process. These quantities have been ... ...

    Abstract Multi-state models are often used for modeling complex event history data. In these models the estimation of the transition probabilities is of particular interest, since they allow for long-term predictions of the process. These quantities have been traditionally estimated by the Aalen-Johansen estimator, which is consistent if the process is Markov. Several non-Markov estimators have been proposed in the recent literature, and their superiority with respect to the Aalen-Johansen estimator has been proved in situations in which the Markov condition is strongly violated. However, the existing estimators have the drawback of requiring that the support of the censoring distribution contains the support of the lifetime distribution, which is not often the case. In this article, we propose two new methods for estimating the transition probabilities in the progressive illness-death model. Some asymptotic results are derived. The proposed estimators are consistent regardless the Markov condition and the referred assumption about the censoring support. We explore the finite sample behavior of the estimators through simulations. The main conclusion of this piece of research is that the proposed estimators are much more efficient than the existing non-Markov estimators in most cases. An application to a clinical trial on colon cancer is included. Extensions to progressive processes beyond the three-state illness-death model are discussed.
    MeSH term(s) Algorithms ; Biometry ; Colonic Neoplasms/mortality ; Colonic Neoplasms/surgery ; Computer Simulation ; Humans ; Kaplan-Meier Estimate ; Markov Chains ; Models, Statistical ; Probability ; Statistics, Nonparametric ; Stochastic Processes ; Survival Analysis
    Language English
    Publishing date 2015-06
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 213543-7
    ISSN 1541-0420 ; 0099-4987 ; 0006-341X
    ISSN (online) 1541-0420
    ISSN 0099-4987 ; 0006-341X
    DOI 10.1111/biom.12288
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  7. Article ; Online: A method for determining groups in nonparametric regression curves: Application to prefrontal cortex neural activity analysis.

    Roca-Pardiñas, Javier / Ordóñez, Celestino / Machado, Luís Meira

    Mathematical biosciences and engineering : MBE

    2022  Volume 19, Issue 7, Page(s) 6435–6454

    Abstract: Generalized additive models provide a flexible and easily-interpretable method for uncovering a nonlinear relationship between response and covariates. In many situations, the effect of a continuous covariate on the response varies across groups defined ... ...

    Abstract Generalized additive models provide a flexible and easily-interpretable method for uncovering a nonlinear relationship between response and covariates. In many situations, the effect of a continuous covariate on the response varies across groups defined by the levels of a categorical variable. When confronted with a considerable number of groups defined by the levels of the categorical variable and a factor-by-curve interaction is detected in the model, it then becomes important to compare these regression curves. When the null hypothesis of equality of curves is rejected, leading to the clear conclusion that at least one curve is different, we may assume that individuals can be grouped into a number of classes whose members all share the same regression function. We propose a method that allows determining such groups with an automatic selection of their number by means of bootstrapping. The validity and behavior of the proposed method were evaluated through simulation studies. The applicability of the proposed method is illustrated using real data from an experimental study in neurology.
    MeSH term(s) Computer Simulation ; Humans ; Models, Statistical ; Prefrontal Cortex ; Research Design
    Language English
    Publishing date 2022-06-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2265126-3
    ISSN 1551-0018 ; 1551-0018
    ISSN (online) 1551-0018
    ISSN 1551-0018
    DOI 10.3934/mbe.2022302
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Insertion Torque Value and Implant Stability Quotient: Separate Evaluation and Correlation for Different Clinical Parameters.

    da Rocha Ferreira, José Joaquim / Machado, Luís Filipe Meira

    The International journal of oral & maxillofacial implants

    2022  Volume 37, Issue 4, Page(s) 812–822

    Abstract: Purpose: To observe whether the initial implant stability, evaluated by two different methods-the insertion torque value (ITV) and implant stability quotient (ISQ)-may be influenced by different clinical conditions as well as to understand whether it is ...

    Abstract Purpose: To observe whether the initial implant stability, evaluated by two different methods-the insertion torque value (ITV) and implant stability quotient (ISQ)-may be influenced by different clinical conditions as well as to understand whether it is possible to establish an overall positive correlation between both methods and whether the obtained correlation is maintained for each clinical variable under scope.
    Materials and methods: The initial implant stability was evaluated by assessing and recording the ITV and the ISQ for each implant included in the study. The independent evolution of each method was observed considering clinical conditions grouped by gender (male or female), age (≤ 60 or > 60 years), arch (mandible or maxilla), location (incisors, canines and premolars, or molars), implant geometry (aggressive tapered or traditional parallel), diameter (3.5, 3.75, 4.3, or 5 mm), length (≥ 10 or < 10 mm), and immediate implantation (yes or no). The Mann-Whitney-Wilcoxon and Kruskal-Wallis localization tests were used to identify intragroup differences. To determine the level of correlation between both methods, the Spearman rank correlation was used.
    Results: The intragroup comparisons showed that the mandible (P = .03), short implants (P = .03), and delayed implantation (P = .07) subgroups exhibited higher ITVs. The other groups did not show significant differences. The higher ISQ measurements were obtained in the mandible (P = .0002), younger patients (P = .02), diameters of 3.75 mm and 4.3 mm (P = .04), and delayed implantation (P < .0001) subgroups. No differences were found for the other groups. A strong overall correlation (rho = 0.541; P = 8.023e-06) was found between both methods for ITVs up to 40 Ncm once they were accompanied by a linear increase in the ISQ to a value up to 78. From this value, the overall correlation decreased (rho = 0.237; P = .0055). Regarding the clinical conditions, different levels of significant correlations were found for both genders, older patients, maxilla, molar area, aggressive tapered implant geometries, diameters of 4.3 mm, diameters of 5 mm, lengths ≥ 10 mm, and implants placed in healed bone. The other clinical conditions under scope did not exhibit an important correlation between both methods.
    Conclusion: When analyzed separately, clinical conditions such as the arch, implant length and diameter, patient age, and timing of implantation showed an influence on the ITV and the ISQ. An important overall correlation between both methods was found for ITVs of ≤ 40 Ncm. This correlation was maintained for several of the clinical conditions studied.
    MeSH term(s) Animals ; Bicuspid/surgery ; Dental Implantation, Endosseous/methods ; Dental Implants ; Female ; Male ; Mandible/surgery ; Maxilla/surgery ; Torque
    Chemical Substances Dental Implants
    Language English
    Publishing date 2022-07-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 632880-5
    ISSN 1942-4434 ; 0882-2786
    ISSN (online) 1942-4434
    ISSN 0882-2786
    DOI 10.11607/jomi.9346
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: survivalBIV

    Ana Moreira / Luis Meira-Machado

    Journal of Statistical Software, Vol 46, Iss

    Estimation of the Bivariate Distribution Function for Sequentially Ordered Events Under Univariate Censoring

    2012  Volume 13

    Abstract: ... time to weight the bivariate data (de Uña-Alvarez and Meira-Machado 2008 and de Uñ-Alvarez and Amorim ...

    Abstract In many medical studies, patients can experience several events. The times between consecutive events (gap times) are often of interest and lead to problems that have received much attention recently. In this work we consider the estimation of the bivariate distribution function for censored gap times, using survivalBIV a software application for R. Some related problems such as the estimation of the marginal distribution of the second gap time is also discussed. It describes the capabilities of the program for estimating these quantities using four different approaches, all using the Kaplan-Meier estimator of survival. One of these estimators is based on Bayes' theorem and Kaplan-Meier survival function. Two estimators were recently proposed using the Kaplan-Meier estimator pertaining to the distribution of the total time to weight the bivariate data (de Uña-Alvarez and Meira-Machado 2008 and de Uñ-Alvarez and Amorim 2011). The software can also be used to implement the estimator proposed in Lin, Sun, and Ying (1999), which is based on inverse probability of censoring weighted. The software is illustrated using data from a bladder cancer study.
    Keywords censoring ; Kaplan-Meier ; multi-state model ; gap times ; inverse censoring ; Statistics ; HA1-4737 ; Social Sciences ; H ; DOAJ:Statistics ; DOAJ:Mathematics and Statistics
    Subject code 310
    Language English
    Publishing date 2012-01-01T00:00:00Z
    Publisher University of California, Los Angeles
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Nonparametric estimation of time-dependent ROC curves conditional on a continuous covariate.

    Rodríguez-Álvarez, María Xosé / Meira-Machado, Luís / Abu-Assi, Emad / Raposeiras-Roubín, Sergio

    Statistics in medicine

    2016  Volume 35, Issue 7, Page(s) 1090–1102

    Abstract: The receiver-operating characteristic (ROC) curve is the most widely used measure for evaluating the performance of a diagnostic biomarker when predicting a binary disease outcome. The ROC curve displays the true positive rate (or sensitivity) and the ... ...

    Abstract The receiver-operating characteristic (ROC) curve is the most widely used measure for evaluating the performance of a diagnostic biomarker when predicting a binary disease outcome. The ROC curve displays the true positive rate (or sensitivity) and the false positive rate (or 1-specificity) for different cut-off values used to classify an individual as healthy or diseased. In time-to-event studies, however, the disease status (e.g. death or alive) of an individual is not a fixed characteristic, and it varies along the study. In such cases, when evaluating the performance of the biomarker, several issues should be taken into account: first, the time-dependent nature of the disease status; and second, the presence of incomplete data (e.g. censored data typically present in survival studies). Accordingly, to assess the discrimination power of continuous biomarkers for time-dependent disease outcomes, time-dependent extensions of true positive rate, false positive rate, and ROC curve have been recently proposed. In this work, we present new nonparametric estimators of the cumulative/dynamic time-dependent ROC curve that allow accounting for the possible modifying effect of current or past covariate measures on the discriminatory power of the biomarker. The proposed estimators can accommodate right-censored data, as well as covariate-dependent censoring. The behavior of the estimators proposed in this study will be explored through simulations and illustrated using data from a cohort of patients who suffered from acute coronary syndrome.
    MeSH term(s) Acute Coronary Syndrome/diagnosis ; Biomarkers/analysis ; Biostatistics ; Computer Simulation ; False Positive Reactions ; Humans ; Models, Statistical ; Predictive Value of Tests ; ROC Curve ; Statistics, Nonparametric ; Survival Analysis ; Time Factors
    Chemical Substances Biomarkers
    Language English
    Publishing date 2016-03-30
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 843037-8
    ISSN 1097-0258 ; 0277-6715
    ISSN (online) 1097-0258
    ISSN 0277-6715
    DOI 10.1002/sim.6769
    Database MEDical Literature Analysis and Retrieval System OnLINE

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