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BACKGROUND: Previous studies demonstrated limited accuracy of existing guidelines for predicting choledocholithiasis, leading to overutilization of endoscopic retrograde cholangiopancreatography (ERCP). More accurate stratification may improve patient selection for ERCP and allow use of lower-risk modalities. METHODS: A machine learning model was developed using patient information from two published cohort studies that evaluated performance of guidelines in predicting choledocholithiasis. Prediction models were developed using the gradient boosting model (GBM) machine learning method. GBM performance was evaluated using 10-fold cross-validation and area under the receiver operating characteristic curve (AUC). Important predictors of choledocholithiasis were identified based on relative importance in the GBM. RESULTS: 1378 patients (mean age 43.3 years; 61.2% female) were included in the GBM and 59.4% had choledocholithiasis. Eight variables were identified as predictors of choledocholithiasis. The GBM had accuracy of 71.5% (SD 2.5%) (AUC 0.79 [SD 0.06]) and performed better than the 2019 American Society for Gastrointestinal Endoscopy (ASGE) guidelines (accuracy 62.4% [SD 2.6%]; AUC 0.63 [SD 0.03]) and European Society of Gastrointestinal Endoscopy (ESGE) guidelines (accuracy 62.8% [SD 2.6%]; AUC 0.67 [SD 0.02]). The GBM correctly categorized 22% of patients directed to unnecessary ERCP by ASGE guidelines, and appropriately recommended as the next management step 48% of ERCPs incorrectly rejected by ESGE guidelines. CONCLUSIONS: A machine learning-based tool was created, providing real-time, personalized, objective probability of choledocholithiasis and ERCP recommendations. This more accurately directed ERCP use than existing ASGE and ESGE guidelines, and has the potential to reduce morbidity associated with ERCP or missed choledocholithiasis.
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Colangiopancreatografia Retrógrada Endoscópica , Coledocolitíase , Humanos , Feminino , Estados Unidos , Adulto , Masculino , Coledocolitíase/diagnóstico por imagem , Coledocolitíase/cirurgia , Sensibilidade e Especificidade , Endoscopia Gastrointestinal , Tomada de Decisões , Estudos RetrospectivosRESUMO
Mediation analysis is used to investigate the role of intermediate variables (mediators) that lie in the path between an exposure and an outcome variable. While significant research has focused on developing methods for assessing the influence of mediators on the exposure-outcome relationship, current approaches do not easily extend to settings where the mediator is high-dimensional. These situations are becoming increasingly common with the rapid increase of new applications measuring massive numbers of variables, including brain imaging, genomics, and metabolomics. In this work, we introduce a novel machine learning based method for identifying high dimensional mediators. The proposed algorithm iterates between using a machine learning model to map the high-dimensional mediators onto a lower-dimensional space, and using the predicted values as input in a standard three-variable mediation model. Hence, the machine learning model is trained to maximize the likelihood of the mediation model. Importantly, the proposed algorithm is agnostic to the machine learning model that is used, providing significant flexibility in the types of situations where it can be used. We illustrate the proposed methodology using data from two functional Magnetic Resonance Imaging (fMRI) studies. First, using data from a task-based fMRI study of thermal pain, we combine the proposed algorithm with a deep learning model to detect distributed, network-level brain patterns mediating the relationship between stimulus intensity (temperature) and reported pain at the single trial level. Second, using resting-state fMRI data from the Human Connectome Project, we combine the proposed algorithm with a connectome-based predictive modeling approach to determine brain functional connectivity measures that mediate the relationship between fluid intelligence and working memory accuracy. In both cases, our multivariate mediation model links exposure variables (thermal pain or fluid intelligence), high dimensional brain measures (single-trial brain activation maps or resting-state brain connectivity) and behavioral outcomes (pain report or working memory accuracy) into a single unified model. Using the proposed approach, we are able to identify brain-based measures that simultaneously encode the exposure variable and correlate with the behavioral outcome.
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Conectoma , Análise de Mediação , Humanos , Encéfalo/fisiologia , Aprendizado de Máquina , Conectoma/métodos , Algoritmos , Imageamento por Ressonância Magnética/métodosRESUMO
In this manuscript, we consider the problem of relating functional connectivity measurements viewed as statistical distributions to outcomes. We demonstrate the utility of using the distribution of connectivity on a study of resting-state functional magnetic resonance imaging association with an intervention. The method uses the estimated density of connectivity between nodes of interest as a functional covariate. Moreover, we demonstrate the utility of the procedure in an instance where connectivity is naturally considered an outcome by reversing the predictor/response relationship using case/control methodology. The method utilizes the density quantile, the density evaluated at empirical quantiles, instead of the empirical density directly. This improved the performance of the method by highlighting tail behavior, though we emphasize that by being flexible and non-parametric, the technique can detect effects related to the central portion of the density. To demonstrate the method in an application, we consider 47 primary progressive aphasia patients with various levels of language abilities. These patients were randomly assigned to two treatment arms, transcranial direct-current stimulation and language therapy versus sham (language therapy only), in a clinical trial. We use the method to analyze the effect of direct stimulation on functional connectivity. As such, we estimate the density of correlations among the regions of interest and study the difference in the density post-intervention between treatment arms. We discover that it is the tail of the density, rather than the mean or lower order moments of the distribution, that demonstrates a significant impact in the classification. The new approach has several benefits. Among them, it drastically reduces the number of multiple comparisons compared with edge-wise analysis. In addition, it allows for the investigation of the impact of functional connectivity on the outcomes where the connectivity is not geometrically localized.
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Estimulação Transcraniana por Corrente Contínua , Humanos , Estimulação Transcraniana por Corrente Contínua/métodos , Imageamento por Ressonância Magnética/métodos , Cognição , Rede Nervosa/fisiologia , Estimulação Magnética TranscranianaRESUMO
Adolescents who are clinically recovered from concussion continue to show subtle motor impairment on neurophysiological and behavioral measures. However, there is limited information on brain-behavior relationships of persistent motor impairment following clinical recovery from concussion. We examined the relationship between subtle motor performance and functional connectivity of the brain in adolescents with a history of concussion, status post-symptom resolution, and subjective return to baseline. Participants included 27 adolescents who were clinically recovered from concussion and 29 never-concussed, typically developing controls (10-17 years); all participants were examined using the Physical and Neurologic Examination of Subtle Signs (PANESS). Functional connectivity between the default mode network (DMN) or dorsal attention network (DAN) and regions of interest within the motor network was assessed using resting-state functional magnetic resonance imaging (rsfMRI). Compared to controls, adolescents clinically recovered from concussion showed greater subtle motor deficits as evaluated by the PANESS and increased connectivity between the DMN and left lateral premotor cortex. DMN to left lateral premotor cortex connectivity was significantly correlated with the total PANESS score, with more atypical connectivity associated with more motor abnormalities. This suggests that altered functional connectivity of the brain may underlie subtle motor deficits in adolescents who have clinically recovered from concussion. More investigation is required to understand the persistence and longer-term clinical relevance of altered functional connectivity and associated subtle motor deficits to inform whether functional connectivity may serve as an important biomarker related to longer-term outcomes after clinical recovery from concussion.
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Concussão Encefálica , Imageamento por Ressonância Magnética , Humanos , Adolescente , Imageamento por Ressonância Magnética/métodos , Concussão Encefálica/complicações , Concussão Encefálica/diagnóstico por imagem , Encéfalo/diagnóstico por imagem , Mapeamento Encefálico/métodosRESUMO
In this study, a longitudinal regression model for covariance matrix outcomes is introduced. The proposal considers a multilevel generalized linear model for regressing covariance matrices on (time-varying) predictors. This model simultaneously identifies covariate-associated components from covariance matrices, estimates regression coefficients, and captures the within-subject variation in the covariance matrices. Optimal estimators are proposed for both low-dimensional and high-dimensional cases by maximizing the (approximated) hierarchical-likelihood function. These estimators are proved to be asymptotically consistent, where the proposed covariance matrix estimator is the most efficient under the low-dimensional case and achieves the uniformly minimum quadratic loss among all linear combinations of the identity matrix and the sample covariance matrix under the high-dimensional case. Through extensive simulation studies, the proposed approach achieves good performance in identifying the covariate-related components and estimating the model parameters. Applying to a longitudinal resting-state functional magnetic resonance imaging data set from the Alzheimer's Disease (AD) Neuroimaging Initiative, the proposed approach identifies brain networks that demonstrate the difference between males and females at different disease stages. The findings are in line with existing knowledge of AD and the method improves the statistical power over the analysis of cross-sectional data.
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Integrative analysis of multiple data sets has the potential of fully leveraging the vast amount of high throughput biological data being generated. In particular such analysis will be powerful in making inference from publicly available collections of genetic, transcriptomic and epigenetic data sets which are designed to study shared biological processes, but which vary in their target measurements, biological variation, unwanted noise, and batch variation. Thus, methods that enable the joint analysis of multiple data sets are needed to gain insights into shared biological processes that would otherwise be hidden by unwanted intra-data set variation. Here, we propose a method called two-stage linked component analysis (2s-LCA) to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition. The consistency of the proposed method is established and its empirical performance is evaluated via simulation studies. We apply 2s-LCA to jointly analyze four data sets focused on human brain development and identify meaningful patterns of gene expression in human neurogenesis that have shared structure across these data sets.
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Transcriptoma , Simulação por Computador , HumanosRESUMO
BACKGROUND: Attention deficit/hyperactivity disorder (ADHD) is a heterogeneous neurodevelopmental disorder. Integrity of white matter microstructure plays a key role in the neural mechanism of ADHD presentations. However, the relationships between specific behavioural dimensions and white matter microstructure are less well known. This study aimed to identify associations between white matter and a broad set of clinical features across children and adolescent with and without ADHD using a data-driven multivariate approach. METHOD: We recruited a total of 130 children (62 controls and 68 ADHD) and employed regularized generalized canonical correlation analysis to characterize the associations between white matter and a comprehensive set of clinical measures covering three domains, including symptom, cognition and behaviour. We further applied linear discriminant analysis to integrate these associations to explore potential developmental effects. RESULTS: We delineated two brain-behaviour dimensional associations in each domain resulting a total of six multivariate patterns of white matter microstructural alterations linked to hyperactivity-impulsivity and mild affected; executive functions and working memory; externalizing behaviour and social withdrawal, respectively. Apart from executive function and externalizing behaviour sharing similar white matter patterns, all other dimensions linked to a specific pattern of white matter microstructural alterations. The multivariate dimensional association scores showed an overall increase and normalization with age in ADHD group while remained stable in controls. CONCLUSIONS: We found multivariate neurobehavioral associations exist across ADHD and controls, which suggested that multiple white matter patterns underlie ADHD heterogeneity and provided neural bases for more precise diagnosis and individualized treatment.
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Transtorno do Deficit de Atenção com Hiperatividade , Substância Branca , Humanos , Criança , Adolescente , Substância Branca/diagnóstico por imagem , Encéfalo , Função Executiva , CogniçãoRESUMO
Brain segmentation at different levels is generally represented as hierarchical trees. Brain regional atrophy at specific levels was found to be marginally associated with Alzheimer's disease outcomes. In this study, we propose an â1 -type regularization for predictors that follow a hierarchical tree structure. Considering a tree as a directed acyclic graph, we interpret the model parameters from a path analysis perspective. Under this concept, the proposed penalty regulates the total effect of each predictor on the outcome. With regularity conditions, it is shown that under the proposed regularization, the estimator of the model coefficient is consistent in â2 -norm and the model selection is also consistent. When applied to a brain sMRI dataset acquired from the Alzheimer's Disease Neuroimaging Initiative (ADNI), the proposed approach identifies brain regions where atrophy in these regions demonstrates the declination in memory. With regularization on the total effects, the findings suggest that the impact of atrophy on memory deficits is localized from small brain regions, but at various levels of brain segmentation. Data used in preparation of this paper were obtained from the ADNI database.
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Doença de Alzheimer , Humanos , Doença de Alzheimer/diagnóstico por imagem , Doença de Alzheimer/patologia , Encéfalo/diagnóstico por imagem , Encéfalo/patologia , Neuroimagem/métodos , Análise de Regressão , Atrofia/patologiaRESUMO
OBJECTIVES: Generalization (or near-transfer) effects of an intervention to tasks not explicitly trained are the most desirable intervention outcomes. However, they are rarely reported and even more rarely explained. One hypothesis for generalization effects is that the tasks improved share the same brain function/computation with the intervention task. We tested this hypothesis in this study of transcranial direct current stimulation (tDCS) over the left inferior frontal gyrus (IFG) that is claimed to be involved in selective semantic retrieval of information from the temporal lobes. MATERIALS AND METHODS: In this study, we examined whether tDCS over the left IFG in a group of patients with primary progressive aphasia (PPA), paired with a lexical/semantic retrieval intervention (oral and written naming), may specifically improve semantic fluency, a nontrained near-transfer task that relies on selective semantic retrieval, in patients with PPA. RESULTS: Semantic fluency improved significantly more in the active tDCS than in the sham tDCS condition immediately after and two weeks after treatment. This improvement was marginally significant two months after treatment. We also found that the active tDCS effect was specific to tasks that require this IFG computation (selective semantic retrieval) but not to other tasks that may require different computations of the frontal lobes. CONCLUSIONS: We provided interventional evidence that the left IFG is critical for selective semantic retrieval, and tDCS over the left IFG may have a near-transfer effect on tasks that depend on the same computation, even if they are not specifically trained. CLINICAL TRIAL REGISTRATION: The Clinicaltrials.gov registration number for the study is NCT02606422.
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Afasia Primária Progressiva , Estimulação Transcraniana por Corrente Contínua , Humanos , Córtex Pré-Frontal , Semântica , Lobo Temporal , Afasia Primária Progressiva/diagnóstico por imagem , Afasia Primária Progressiva/terapiaRESUMO
In this study, we consider the problem of regressing covariance matrices on associated covariates. Our goal is to use covariates to explain variation in covariance matrices across units. As such, we introduce Covariate Assisted Principal (CAP) regression, an optimization-based method for identifying components associated with the covariates using a generalized linear model approach. We develop computationally efficient algorithms to jointly search for common linear projections of the covariance matrices, as well as the regression coefficients. Under the assumption that all the covariance matrices share identical eigencomponents, we establish the asymptotic properties. In simulation studies, our CAP method shows higher accuracy and robustness in coefficient estimation over competing methods. In an example resting-state functional magnetic resonance imaging study of healthy adults, CAP identifies human brain network changes associated with subject demographics.
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Algoritmos , Imageamento por Ressonância Magnética , Encéfalo/diagnóstico por imagem , Simulação por Computador , Humanos , Modelos LinearesRESUMO
Replicability, the ability to replicate scientific findings, is a prerequisite for scientific discovery and clinical utility. Troublingly, we are in the midst of a replicability crisis. A key to replicability is that multiple measurements of the same item (e.g., experimental sample or clinical participant) under fixed experimental constraints are relatively similar to one another. Thus, statistics that quantify the relative contributions of accidental deviations-such as measurement error-as compared to systematic deviations-such as individual differences-are critical. We demonstrate that existing replicability statistics, such as intra-class correlation coefficient and fingerprinting, fail to adequately differentiate between accidental and systematic deviations in very simple settings. We therefore propose a novel statistic, discriminability, which quantifies the degree to which an individual's samples are relatively similar to one another, without restricting the data to be univariate, Gaussian, or even Euclidean. Using this statistic, we introduce the possibility of optimizing experimental design via increasing discriminability and prove that optimizing discriminability improves performance bounds in subsequent inference tasks. In extensive simulated and real datasets (focusing on brain imaging and demonstrating on genomics), only optimizing data discriminability improves performance on all subsequent inference tasks for each dataset. We therefore suggest that designing experiments and analyses to optimize discriminability may be a crucial step in solving the replicability crisis, and more generally, mitigating accidental measurement error.
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Conectoma , Genoma , Artefatos , Mapeamento Encefálico/métodos , Conjuntos de Dados como Assunto , Humanos , Reprodutibilidade dos TestesRESUMO
In this study, we propose a two-stage procedure for hypothesis testing, where the first stage is conventional hypothesis testing and the second is an equivalence testing procedure using an introduced empirical equivalence bound (EEB). In 2016, the American Statistical Association released a policy statement on P-values to clarify the proper use and interpretation in response to the criticism of reproducibility and replicability in scientific findings. A recent solution to improve reproducibility and transparency in statistical hypothesis testing is to integrate P-values (or confidence intervals) with practical or scientific significance. Similar ideas have been proposed via the equivalence test, where the goal is to infer equality under a presumption (null) of inequality of parameters. However, the definition of scientific significance/equivalence can sometimes be ill-justified and subjective. To circumvent this drawback, we introduce the B-value and the EEB, which are both estimated from the data. Performing a second-stage equivalence test, our procedure offers an opportunity to improve the reproducibility of findings across studies.
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Projetos de Pesquisa , Humanos , Reprodutibilidade dos TestesRESUMO
Multi-institutional brain imaging studies have emerged to resolve conflicting results among individual studies. However, adjusting multiple variables at the technical and cohort levels is challenging. Therefore, it is important to explore approaches that provide meaningful results from relatively small samples at institutional levels. We studied 87 first episode psychosis (FEP) patients and 62 healthy subjects by combining supervised integrated factor analysis (SIFA) with a novel pipeline for automated structure-based analysis, an efficient and comprehensive method for dimensional data reduction that our group recently established. We integrated multiple MRI features (volume, DTI indices, resting state fMRI-rsfMRI) in the whole brain of each participant in an unbiased manner. The automated structure-based analysis showed widespread DTI abnormalities in FEP and rs-fMRI differences between FEP and healthy subjects mostly centered in thalamus. The combination of multiple modalities with SIFA was more efficient than the use of single modalities to stratify a subgroup of FEP (individuals with schizophrenia or schizoaffective disorder) that had more robust deficits from the overall FEP group. The information from multiple MRI modalities and analytical methods highlighted the thalamus as significantly abnormal in FEP. This study serves as a proof-of-concept for the potential of this methodology to reveal disease underpins and to stratify populations into more homogeneous sub-groups.
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Imageamento por Ressonância Magnética , Neuroimagem , Transtornos Psicóticos , Esquizofrenia , Tálamo , Adolescente , Adulto , Conectoma , Imagem de Tensor de Difusão , Feminino , Humanos , Masculino , Estudo de Prova de Conceito , Transtornos Psicóticos/diagnóstico por imagem , Transtornos Psicóticos/patologia , Transtornos Psicóticos/fisiopatologia , Esquizofrenia/diagnóstico por imagem , Esquizofrenia/patologia , Esquizofrenia/fisiopatologia , Tálamo/diagnóstico por imagem , Tálamo/patologia , Tálamo/fisiopatologia , Adulto JovemRESUMO
Background Resting-state functional MRI (rs-fMRI) is a potential alternative to task-based functional MRI (tb-fMRI) for somatomotor network (SMN) identification. Brain networks can also be generated from tb-fMRI by using independent component analysis (ICA). Purpose To investigate whether the SMN can be identified by using ICA from a language task without a motor component, the sentence completion functional MRI (sc-fMRI) task, compared with rs-fMRI. Materials and Methods The sc-fMRI and rs-fMRI scans in patients who underwent presurgical brain mapping between 2012 and 2016 were analyzed, using the same imaging parameters (other than scanning time) on a 3.0-T MRI scanner. ICA was performed on rs-fMRI and sc-fMRI scans with use of a tool to separate data sets into their spatial and temporal components. Two neuroradiologists independently determined the presence of the dorsal SMN (dSMN) and ventral SMN (vSMN) on each study. Groups were compared by using t tests, and logistic regression was performed to identify predictors of the presence of SMNs. Results One hundred patients (mean age, 40.9 years ± 14.8 [standard deviation]; 61 men) were evaluated. The dSMN and vSMN were identified in 86% (86 of 100) and 76% (76 of 100) of rs-fMRI scans and 85% (85 of 100) and 69% (69 of 100) of sc-fMRI scans, respectively. The concordance between rs-fMRI and sc-fMRI for presence of dSMN and vSMN was 75% (75 of 100 patients) and 53% (53 of 100 patients), respectively. In 10 of 14 patients (71%) where rs-fMRI did not show the dSMN, sc-fMRI demonstrated it. This rate was 67% for the vSMN (16 of 24 patients). Conclusion In the majority of patients, independent component analysis of sentence completion task functional MRI scans reliably demonstrated the somatomotor network compared with resting-state functional MRI scans. Identifying target networks with a single sentence completion scan could reduce overall functional MRI scanning times by eliminating the need for separate motor tasks. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Field and Birn in this issue.
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Mapeamento Encefálico/métodos , Neoplasias Encefálicas/diagnóstico por imagem , Imageamento por Ressonância Magnética/métodos , Córtex Motor/diagnóstico por imagem , Adulto , Encéfalo/diagnóstico por imagem , Feminino , Humanos , Idioma , Masculino , Reprodutibilidade dos Testes , DescansoRESUMO
With advancements in technology, the collection of multiple types of measurements on a common set of subjects is becoming routine in science. Some notable examples include multimodal neuroimaging studies for the simultaneous investigation of brain structure and function and multi-omics studies for combining genetic and genomic information. Integrative analysis of multimodal data allows scientists to interrogate new mechanistic questions. However, the data collection and generation of integrative hypotheses is outpacing available methodology for joint analysis of multimodal measurements. In this article, we study high-dimensional multimodal data integration in the context of mediation analysis. We aim to understand the roles that different data modalities play as possible mediators in the pathway between an exposure variable and an outcome. We propose a mediation model framework with two data types serving as separate sets of mediators and develop a penalized optimization approach for parameter estimation. We study both the theoretical properties of the estimator through an asymptotic analysis and its finite-sample performance through simulations. We illustrate our method with a multimodal brain pathway analysis having both structural and functional connectivity as mediators in the association between sex and language processing.
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Encéfalo , Neuroimagem , Encéfalo/diagnóstico por imagem , HumanosRESUMO
We consider the problem of jointly modeling multiple covariance matrices by partial common principal component analysis (PCPCA), which assumes a proportion of eigenvectors to be shared across covariance matrices and the rest to be individual-specific. This paper proposes consistent estimators of the shared eigenvectors in the PCPCA as the number of matrices or the number of samples to estimate each matrix goes to infinity. We prove such asymptotic results without making any assumptions on the ranks of eigenvalues that are associated with the shared eigenvectors. When the number of samples goes to infinity, our results do not require the data to be Gaussian distributed. Furthermore, this paper introduces a sequential testing procedure to identify the number of shared eigenvectors in the PCPCA. In simulation studies, our method shows higher accuracy in estimating the shared eigenvectors than competing methods. Applied to a motor-task functional magnetic resonance imaging data set, our estimator identifies meaningful brain networks that are consistent with current scientific understandings of motor networks during a motor paradigm.
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Encéfalo , Imageamento por Ressonância Magnética , Simulação por Computador , Análise de Componente PrincipalRESUMO
Allografts from living kidney donors with hypertension may carry subclinical kidney disease from the donor to the recipient and, thus, lead to adverse recipient outcomes. We examined eGFR trajectories and all-cause allograft failure in recipients from donors with versus without hypertension, using mixed-linear and Cox regression models stratified by donor age. We studied a US cohort from 1/1/2005 to 6/30/2017; 49 990 recipients of allografts from younger (<50 years old) donors including 597 with donor hypertension and 21 130 recipients of allografts from older (≥50 years old) donors including 1441 with donor hypertension. Donor hypertension was defined as documented predonation use of antihypertensive therapy. Among recipients from younger donors with versus without hypertension, the annual eGFR decline was -1.03 versus -0.53 ml/min/m2 (P = 0.002); 13-year allograft survival was 49.7% vs. 59.0% (adjusted allograft failure hazard ratio [aHR] 1.23; 95% CI 1.05-1.43; P = 0.009). Among recipients from older donors with versus without hypertension, the annual eGFR decline was -0.67 versus -0.66 ml/min/m2 (P = 0.9); 13-year allograft survival was 48.6% versus 52.6% (aHR 1.05; 95% CI 0.94-1.17; P = 0.4). In secondary analyses, our inferences remained similar for risk of death-censored allograft failure and mortality. Hypertension in younger, but not older, living kidney donors is associated with worse recipient outcomes.
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Hipertensão , Transplante de Rim , Aloenxertos , Estudos de Coortes , Sobrevivência de Enxerto , Humanos , Rim , Transplante de Rim/efeitos adversos , Doadores Vivos , Pessoa de Meia-Idade , Estudos Retrospectivos , Doadores de Tecidos , Resultado do TratamentoRESUMO
Neuroconductor (https://neuroconductor.org) is an open-source platform for rapid testing and dissemination of reproducible computational imaging software. The goals of the project are to: (i) provide a centralized repository of R software dedicated to image analysis, (ii) disseminate software updates quickly, (iii) train a large, diverse community of scientists using detailed tutorials and short courses, (iv) increase software quality via automatic and manual quality controls, and (v) promote reproducibility of image data analysis. Based on the programming language R (https://www.r-project.org/), Neuroconductor starts with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing. We provide a description of the purpose of Neuroconductor and the user and developer experience.
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Diagnóstico por Imagem/métodos , Interpretação de Imagem Assistida por Computador/métodos , Processamento de Imagem Assistida por Computador/métodos , Neuroimagem/métodos , Software , Feminino , Humanos , MasculinoRESUMO
An increasing number of studies claim machine learning (ML) predicts transplant outcomes more accurately. However, these claims were possibly confounded by other factors, namely, supplying new variables to ML models. To better understand the prospects of ML in transplantation, we compared ML to conventional regression in a "common" analytic task: predicting kidney transplant outcomes using national registry data. We studied 133 431 adult deceased-donor kidney transplant recipients between 2005 and 2017. Transplant centers were randomly divided into 70% training set (190 centers/97 787 recipients) and 30% validation set (82 centers/35 644 recipients). Using the training set, we performed regression and ML procedures [gradient boosting (GB) and random forests (RF)] to predict delayed graft function, one-year acute rejection, death-censored graft failure C, all-cause graft failure, and death. Their performances were compared on the validation set using -statistics. In predicting rejection, regression (C = 0.601 0.6110.621 ) actually outperformed GB (C = 0.581 0.5910.601 ) and RF (C = 0.569 0.5790.589 ). For all other outcomes, the C-statistics were nearly identical across methods (delayed graft function, 0.717-0.723; death-censored graft failure, 0.637-0.642; all-cause graft failure, 0.633-0.635; and death, 0.705-0.708). Given its shortcomings in model interpretability and hypothesis testing, ML is advantageous only when it clearly outperforms conventional regression; in the case of transplant outcomes prediction, ML seems more hype than helpful.
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Rejeição de Enxerto , Transplante de Rim , Adulto , Estudos de Coortes , Sobrevivência de Enxerto , Humanos , Aprendizado de Máquina , Doadores de Tecidos , Resultado do TratamentoRESUMO
Causal mediation analysis aims to quantify the intermediate effect of a mediator on the causal pathway from treatment to outcome. When dealing with multiple mediators, which are potentially causally dependent, the possible decomposition of pathway effects grows exponentially with the number of mediators. An existing approach incorporated the principal component analysis (PCA) to address this challenge based on the fact that the transformed mediators are conditionally independent given the orthogonality of the principal components (PCs). However, the transformed mediator PCs, which are linear combinations of original mediators, can be difficult to interpret. A sparse high-dimensional mediation analysis approach is proposed which adopts the sparse PCA method to the mediation setting. The proposed approach is applied to a task-based functional magnetic resonance imaging study, illustrating its ability to detect biologically meaningful results related to an identified mediator.