@article {793, title = {Multilevel sparse functional principal component analysis.}, journal = {Stat}, volume = {3}, year = {2014}, month = {2014 Jan 29}, pages = {126-143}, abstract = {

We consider analysis of sparsely sampled multilevel functional data, where the basic observational unit is a function and data have a natural hierarchy of basic units. An example is when functions are recorded at multiple visits for each subject. Multilevel functional principal component analysis (MFPCA; Di et al. 2009) was proposed for such data when functions are densely recorded. Here we consider the case when functions are sparsely sampled and may contain only a few observations per function. We exploit the multilevel structure of covariance operators and achieve data reduction by principal component decompositions at both between and within subject levels. We address inherent methodological differences in the sparse sampling context to: 1) estimate the covariance operators; 2) estimate the functional principal component scores; 3) predict the underlying curves. Through simulations the proposed method is able to discover dominating modes of variations and reconstruct underlying curves well even in sparse settings. Our approach is illustrated by two applications, the Sleep Heart Health Study and eBay auctions.

}, issn = {0038-9986}, doi = {10.1002/sta4.50}, author = {Di, Chongzhi and Crainiceanu, Ciprian M and Jank, Wolfgang S} } @article {709, title = {Microcystic macular oedema, thickness of the inner nuclear layer of the retina, and disease characteristics in multiple sclerosis: a retrospective study.}, journal = {Lancet Neurol}, volume = {11}, year = {2012}, month = {2012 Nov}, pages = {963-72}, abstract = {

BACKGROUND: Microcystic macular oedema (MMO) of the retinal inner nuclear layer (INL) has been identified in patients with multiple sclerosis (MS) by use of optical coherence tomography (OCT). We aimed to determine whether MMO of the INL, and increased thickness of the INL are associated with disease activity or disability progression.

METHODS: This retrospective study was done at the Johns Hopkins Hospital (Baltimore, MD, USA), between September, 2008, and March, 2012. Patients with MS and healthy controls underwent serial OCT scans and clinical assessments including visual function. OCT scanning, including automated intraretinal layer segmentation, yielded thicknesses of the retinal nerve fibre layer, the ganglion cell layer plus inner plexiform layer, the INL plus outer plexiform layer (the combined thickness of these layers was used as a surrogate measure of INL thickness), and the outer nuclear layer. Patients with MS also underwent annual brain MRI scans. Disability scores were compared with the Wilcoxon rank-sum test. Mixed-effects linear regression was used to compare OCT measures and letter-acuity scores. Logistic regression was used to examine the relations of baseline OCT thicknesses with clinical and radiological parameters.

FINDINGS: 164 patients with MS and 60 healthy controls were assessed. Mean follow-up was 25{\textperiodcentered}8 months (SD 9{\textperiodcentered}1) for patients with MS and 22{\textperiodcentered}4 months (11{\textperiodcentered}4) for healthy controls. Ten (6\%) patients with MS had MMO during at least one study visit; MMO was visible at baseline in four of these patients. Healthy controls did not have MMO. Patients with MS and MMO had higher baseline MS severity scores (median 5{\textperiodcentered}93 [range 2{\textperiodcentered}44-8{\textperiodcentered}91]) than those who did not have MMO at any time during the study (151 patients; 3{\textperiodcentered}81 [0{\textperiodcentered}13-9{\textperiodcentered}47]; p=0{\textperiodcentered}032), although expanded disability status scale (EDSS) scores were not significantly different (5{\textperiodcentered}2 [1{\textperiodcentered}0-6{\textperiodcentered}5] for patients with MS and MMO vs 2{\textperiodcentered}5 [0{\textperiodcentered}0-8{\textperiodcentered}0] for those without MMO; p=0{\textperiodcentered}097). The eyes of patients with MS and MMO (12 eyes) versus those without MMO (302 eyes) had lower letter-acuity scores (100\% contrast, p=0{\textperiodcentered}017; 2{\textperiodcentered}5\% contrast, p=0{\textperiodcentered}031; 1{\textperiodcentered}25\% contrast, p=0{\textperiodcentered}014), and increased INL thicknesses (p=0{\textperiodcentered}003) at baseline. Increased baseline INL thickness in patients with MS was associated with the development of contrast-enhancing lesions (p=0{\textperiodcentered}007), new T2 lesions (p=0{\textperiodcentered}015), EDSS progression (p=0{\textperiodcentered}034), and relapses in patients with relapsing-remitting MS (p=0{\textperiodcentered}008) during the study. MMO was not associated with disease activity during follow-up.

INTERPRETATION: Increased INL thickness on OCT is associated with disease activity in MS. If this finding is confirmed, INL thickness could be a useful predictor of disease progression in patients with MS.

FUNDING: National Multiple Sclerosis Society, National Eye Institute, Braxton Debbie Angela Dillon and Skip Donor Advisor Fund.

}, keywords = {Adult, Cohort Studies, Female, Follow-Up Studies, Humans, Macular Edema, Male, Middle Aged, Multiple Sclerosis, Retina, Retinal Ganglion Cells, Retrospective Studies, Tomography, Optical Coherence}, issn = {1474-4465}, doi = {10.1016/S1474-4422(12)70213-2}, author = {Saidha, Shiv and Sotirchos, Elias S and Ibrahim, Mohamed A and Crainiceanu, Ciprian M and Gelfand, Jeffrey M and Sepah, Yasir J and Ratchford, John N and Oh, Jiwon and Seigo, Michaela A and Newsome, Scott D and Balcer, Laura J and Frohman, Elliot M and Green, Ari J and Nguyen, Quan D and Calabresi, Peter A} } @article {pmid22241689, title = {Mixed effect Poisson log-linear models for clinical and epidemiological sleep hypnogram data}, journal = {Stat Med}, volume = {31}, number = {9}, year = {2012}, month = {Apr}, pages = {855{\textendash}870}, author = {Swihart, B and Caffo, B and Crainiceanu, C and Punjabi, N.M.} } @article {swihartTransition, title = {Models of sleep hypnograms scalable to epidemiological studies}, journal = {Tentatively accepted in Statistics in Medicine}, year = {2012}, author = {Swihart, B and Caffo, B and Crainiceanu, C and Punjabi, N} } @article {barber, title = {Motor "dexterity"?: evidence that left hemisphere lateralization of motor circuit connectivity is associated with better motor performance in children}, journal = {Cerebral Cortex}, year = {2012}, author = {Barber, A and Srinivasan, P and Joel, S. and Caffo, B and Pekar, J and Mostofsky, S} } @article {813, title = {Movelets: A dictionary of movement.}, journal = {Electron J Stat}, volume = {6}, year = {2012}, month = {2012}, pages = {559-578}, abstract = {

Recent technological advances provide researchers with a way of gathering real-time information on an individual{\textquoteright}s movement through the use of wearable devices that record acceleration. In this paper, we propose a method for identifying activity types, like walking, standing, and resting, from acceleration data. Our approach decomposes movements into short components called "movelets", and builds a reference for each activity type. Unknown activities are predicted by matching new movelets to the reference. We apply our method to data collected from a single, three-axis accelerometer and focus on activities of interest in studying physical function in elderly populations. An important technical advantage of our methods is that they allow identification of short activities, such as taking two or three steps and then stopping, as well as low frequency rare(compared with the whole time series) activities, such as sitting on a chair. Based on our results we provide simple and actionable recommendations for the design and implementation of large epidemiological studies that could collect accelerometry data for the purpose of predicting the time series of activities and connecting it to health outcomes.

}, issn = {1935-7524}, doi = {10.1214/12-EJS684}, author = {Bai, Jiawei and Goldsmith, Jeff and Caffo, Brian and Glass, Thomas A and Crainiceanu, Ciprian M} } @article {BaGoCaGlCr2012, title = {Movelets: A dictionary of movement}, journal = {Electronic Journal of Statistics}, volume = {6}, year = {2012}, pages = {559-578}, issn = {1935-7524}, doi = {10.1214/12-EJS684}, author = {Bai, J and Goldsmith, J and Caffo, B and Glass, T and Crainiceanu, C} } @article {AJT:AJT3735, title = {MELD Exceptions and Rates of Waiting List Outcomes}, journal = {American Journal of Transplantation}, volume = {11}, number = {11}, year = {2011}, pages = {2362{\textendash}2371}, publisher = {Blackwell Publishing Inc}, keywords = {Liver transplantation, MELD score, organ allocation}, issn = {1600-6143}, doi = {10.1111/j.1600-6143.2011.03735.x}, url = {http://dx.doi.org/10.1111/j.1600-6143.2011.03735.x}, author = {Massie, A and Caffo, B and Gentry, S and Hall, E and Axelrod, D and Lentine, K and Schnitzler, M and Gheorghian, A and Salvalaggio, P and Segev, D} } @article {Mondul2011e6, title = {Minimal detection bias in the inverse association between statin drug use and advanced prostate cancer risk: A simulation study}, journal = {Cancer Epidemiology, PMCID: PMC3142317}, volume = {35}, number = {4}, year = {2011}, pages = {e6 - e11}, keywords = {Prostate-specific antigen}, issn = {1877-7821}, doi = {DOI: 10.1016/j.canep.2010.11.005}, url = {http://www.sciencedirect.com/science/article/pii/S1877782110002055}, author = {Alison M. Mondul and Caffo, B and Elizabeth A. Platz} } @article {pmid22050118, title = {Modeling Functional Data with Spatially Heterogeneous Shape Characteristics}, journal = {Biometrics}, year = {2011}, month = {Nov}, author = {Staicu, A. M. and Crainiceanu, C and Reich, D S and Ruppert, D.} } @article {vadimHDMFPCA, title = {Multilevel functional principal component analysis for high-dimensional data}, journal = {Journal of Computational and Graphical Statistics, NIMHID: 306063}, volume = {20}, number = {4}, year = {2011}, pages = {852{\textendash}873}, author = {Zipunnikov, V. and Caffo, B and Crainiceanu, C and Yousem, D and Davatzikos, C. and Schwartz, B} } @article {reich2, title = {MRI of the Corpus Callosum in Multiple Sclerosis: Association with Disability}, journal = {Multiple Sclerosis, PMCID: PMC2820126}, volume = {16}, number = {2}, year = {2010}, pages = {166{\textendash}177}, author = {Ozturk, A and Smith, S and Gordon-Lipkin, E and Harrison, D and Shiee, N and Pham, D and Caffo, B and Calabresi, P and Reich, D.} } @article {pmid20049214, title = {Mercury induces an unopposed inflammatory response in human peripheral blood mononuclear cells in vitro}, journal = {Environ. Health Perspect.}, volume = {117}, number = {12}, year = {2009}, month = {Dec}, pages = {1932{\textendash}1938}, author = {Gardner, R. M. and Nyland, J. F. and Evans, S. L. and Wang, S. B. and Doyle, K. M. and Crainiceanu, C and Silbergeld, E. K.} } @article {lindquist09, title = {Modeling the Hemodynamic Response Function in fMRI: Efficiency, Bias and Mis-modeling}, journal = {NeuroImage}, volume = {45}, year = {2009}, pages = {S187-S198}, author = {Lindquist, Martin A and Loh, J.M. and Atlas, L. and Wager, T.D.} } @article {su2009modified, title = {Modified test statistics by inter-voxel variance shrinkage with an application to fMRI}, journal = {Biostatistics, NIHMSID: 316409}, volume = {10}, number = {2}, year = {2009}, pages = {219-227}, author = {Su, S and Caffo, B and Garrett-Mayer, E and Bassett, S} } @article {di2009multilevel, title = {Multilevel functional principal component analysis}, journal = {Annals of Applied Statistics, PMCID: PMC2835171}, volume = {3}, number = {1}, year = {2009}, pages = {458-488}, author = {Di, C and Crainiceanu, C and Caffo, B and Punjabi, N} } @article {choi2008mechanistic, title = {A mechanistic latent variable model for estimating drug concentrations in the male genital tract: A case study in drug kinetics}, journal = {Statistics in Medicine, PMCID: PMC2763330}, volume = {27}, number = {14}, year = {2008}, pages = {2697{\textendash}2714}, publisher = {John Wiley \& Sons, Ltd Chichester, UK}, author = {Choi, L and Caffo, B and Rohde, C and Ndovi, T and Hendrix, C} } @article {pmid18552590, title = {Model selection and health effect estimation in environmental epidemiology}, journal = {Epidemiology}, volume = {19}, number = {4}, year = {2008}, month = {Jul}, pages = {558{\textendash}560}, author = {Dominici, F. and Wang, C. and Crainiceanu, C and Parmigiani, G.} } @article {wager2007meta, title = {Meta-analysis of functional neuroimaging data: current and future directions}, journal = {Social Cognitive and Affective Neuroscience}, volume = {2}, number = {2}, year = {2007}, pages = {150{\textendash}158}, publisher = {Oxford University Press}, author = {Wager, Tor D and Lindquist, Martin A and Kaplan, Lauren} } @article {lindquist2007modeling, title = {Modeling state-related fMRI activity using change-point theory}, journal = {NeuroImage}, volume = {35}, number = {3}, year = {2007}, pages = {1125{\textendash}1141}, publisher = {Elsevier}, author = {Lindquist, Martin A and Waugh, Christian and Wager, Tor D} } @article {caffo2003monte, title = {Monte Carlo conditional inference for log-linear and logistic models: a survey of current methodology}, journal = {Statistical Methods in Medical Research}, volume = {12}, number = {2}, year = {2003}, pages = {109}, author = {Caffo, B and Booth, J} } @article {agresti2002measures, title = {Measures of relative model fit}, journal = {Computational Statistics and Data Analysis}, volume = {39}, number = {2}, year = {2002}, pages = {127{\textendash}136}, publisher = {Elsevier}, author = {Agresti, A and Caffo, B} } @article {caffo2001markov, title = {A Markov chain Monte Carlo algorithm for approximating exact conditional probabilities}, journal = {Journal of Computational and Graphical Statistics}, volume = {10}, number = {4}, year = {2001}, pages = {730{\textendash}745}, publisher = {ASA}, author = {Caffo, B and Booth, J} } @article {hartzel2001multinomial, title = {Multinomial logit random effects models}, journal = {Statistical Modelling}, volume = {1}, number = {2}, year = {2001}, pages = {81}, author = {Hartzel, J and Agresti, A and Caffo, B} }