@article {819, title = {Analytic programming with FMRI data: a quick-start guide for statisticians using R.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e89470}, abstract = {

Functional magnetic resonance imaging (fMRI) is a thriving field that plays an important role in medical imaging analysis, biological and neuroscience research and practice. This manuscript gives a didactic introduction to the statistical analysis of fMRI data using the R project, along with the relevant R code. The goal is to give statisticians who would like to pursue research in this area a quick tutorial for programming with fMRI data. References of relevant packages and papers are provided for those interested in more advanced analysis.

}, keywords = {Brain, brain mapping, Humans, Magnetic Resonance Imaging, Programming Languages}, issn = {1932-6203}, doi = {10.1371/journal.pone.0089470}, author = {Eloyan, Ani and Li, Shanshan and Muschelli, John and Pekar, Jim J and Mostofsky, Stewart H and Caffo, Brian S} } @article {797, title = {Biomarkers of vascular calcification and mortality in patients with ESRD.}, journal = {Clin J Am Soc Nephrol}, volume = {9}, year = {2014}, month = {2014 Apr}, pages = {745-55}, abstract = {

BACKGROUND: Vascular calcification is common among patients undergoing dialysis and is associated with mortality. Factors such as osteoprotegerin (OPG), osteopontin (OPN), bone morphogenic protein-7 (BMP-7), and fetuin-A are involved in vascular calcification.

DESIGN, SETTING, PARTICIPANTS, \& MEASUREMENTS: OPG, OPN, BMP-7, and fetuin-A were measured in blood samples from 602 incident dialysis patients recruited from United States dialysis centers between 1995 and 1998 as part of the Choices for Healthy Outcomes In Caring for ESRD Study. Their association with all-cause and cardiovascular mortality were assessed using Cox proportional hazards models adjusted for demographic characteristics, comorbidity, serum phosphate, and calcium. An interaction with diabetes was tested because of its known association with vascular calcification. Predictive accuracy of selected biomarkers was explored by C-statistics in nested models with training and validation subcohorts.

RESULTS: Higher OPG and lower fetuin-A levels were associated with higher mortality over up to 13 years of follow-up (median, 3.4 years). The adjusted hazard ratios (HR) for highest versus lowest tertile were 1.49 (95\% confidence interval [95\% CI], 1.08 to 2.06) for OPG and 0.69 (95\% CI, 0.52 to 0.92) for fetuin-A. In stratified models, the highest tertile of OPG was associated with higher mortality among patients without diabetes (HR, 2.42; 95\% CI, 1.35 to 4.34), but not patients with diabetes (HR, 1.26; 95\% CI, 0.82 to 1.93; P for interaction=0.001). In terms of cardiovascular mortality, higher fetuin-A was associated with lower risk (HR, 0.85 per 0.1 g/L: 95\% CI, 0.75 to 0.96). In patients without diabetes, higher OPG was associated with greater risk (HR for highest versus lowest tertile, 2.91; 95\% CI, 1.06 to 7.99), but not in patients with diabetes or overall. OPN and BMP-7 were not independently associated with outcomes overall. The addition of OPG and fetuin-A did not significantly improve predictive accuracy of mortality.

CONCLUSIONS: OPG and fetuin-A may be risk factors for all-cause and cardiovascular mortality in patients undergoing dialysis, but do not improve risk prediction.

}, issn = {1555-905X}, doi = {10.2215/CJN.05450513}, author = {Scialla, Julia J and Kao, W H Linda and Crainiceanu, Ciprian and Sozio, Stephen M and Oberai, Pooja C and Shafi, Tariq and Coresh, Josef and Powe, Neil R and Plantinga, Laura C and Jaar, Bernard G and Parekh, Rulan S} } @article {831, title = {Disruption of functional organization within the primary motor cortex in children with autism.}, journal = {Hum Brain Mapp}, volume = {35}, year = {2014}, month = {2014 Feb}, pages = {567-80}, abstract = {

Accumulating evidence suggests that motor impairments are prevalent in autism spectrum disorder (ASD), relate to the social and communicative deficits at the core of the diagnosis and may reflect abnormal connectivity within brain networks underlying motor control and learning. Parcellation of resting-state functional connectivity data using spectral clustering approaches has been shown to be an effective means of visualizing functional organization within the brain but has most commonly been applied to explorations of normal brain function. This article presents a parcellation of a key area of the motor network, the primary motor cortex (M1), a key area of the motor control network, in adults, typically developing (TD) children and children with ASD and introduces methods for selecting the number of parcels, matching parcels across groups and testing group differences. The parcellation is based solely on patterns of connectivity between individual M1 voxels and all voxels outside of M1, and within all groups, a gross dorsomedial to ventrolateral organization emerged within M1 which was left-right symmetric. Although this gross organizational scheme was present in both groups of children, statistically significant group differences in the size and segregation of M1 parcels within regions of the motor homunculus corresponding to the upper and lower limbs were observed. Qualitative comparison of the M1 parcellation for children with ASD with that of younger and older TD children suggests that these organizational differences, with a lack of differentiation between lower limb/trunk regions and upper limb/hand regions, may be due, at least in part, to a delay in functional specialization within the motor cortex.

}, keywords = {Adult, Autistic Disorder, brain mapping, Child, Developmental Disabilities, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Motor Cortex, Oxygen, Young Adult}, issn = {1097-0193}, doi = {10.1002/hbm.22188}, author = {Nebel, Mary Beth and Joel, Suresh E and Muschelli, John and Barber, Anita D and Caffo, Brian S and Pekar, James J and Mostofsky, Stewart H} } @article {815, title = {Neuroinflammation and brain atrophy in former NFL players: An in vivo multimodal imaging pilot study.}, journal = {Neurobiol Dis}, volume = {74C}, year = {2014}, month = {2014 Nov 7}, pages = {58-65}, abstract = {

There are growing concerns about potential delayed, neuropsychiatric consequences (e.g, cognitive decline, mood or anxiety disorders) of sports-related traumatic brain injury (TBI). Autopsy studies of brains from a limited number of former athletes have described characteristic, pathologic changes of chronic traumatic encephalopathy (CTE) leading to questions about the relationship between these pathologic and the neuropsychiatric disturbances seen in former athletes. Research in this area will depend on in vivo methods that characterize molecular changes in the brain, linking CTE and other sports-related pathologies with delayed emergence of neuropsychiatric symptoms. In this pilot project we studied former National Football League (NFL) players using new neuroimaging techniques and clinical measures of cognitive functioning. We hypothesized that former NFL players would show molecular and structural changes in medial temporal and parietal lobe structures as well as specific cognitive deficits, namely those of verbal learning and memory. We observed a significant increase in binding of [(11)C]DPA-713 to the translocator protein (TSPO), a marker of brain injury and repair, in several brain regions, such as the supramarginal gyrus and right amygdala, in 9 former NFL players compared to 9 age-matched, healthy controls. We also observed significant atrophy of the right hippocampus. Finally, we report that these same former players had varied performance on a test of verbal learning and memory, suggesting that these molecular and pathologic changes may play a role in cognitive decline. These results suggest that localized brain injury and repair, indicated by increased [(11)C]DPA-713 binding to TSPO, may be linked to history of NFL play. [(11)C]DPA-713 PET is a promising new tool that can be used in future study design to examine further the relationship between TSPO expression in brain injury and repair, selective regional brain atrophy, and the potential link to deficits in verbal learning and memory after NFL play.

}, issn = {1095-953X}, doi = {10.1016/j.nbd.2014.10.019}, author = {Coughlin, Jennifer M and Wang, Yuchuan and Munro, Cynthia A and Ma, Shuangchao and Yue, Chen and Chen, Shaojie and Airan, Raag and Kim, Pearl K and Adams, Ashley V and Garcia, Cinthya and Higgs, Cecilia and Sair, Haris I and Sawa, Akira and Smith, Gwenn and Lyketsos, Constantine G and Caffo, Brian and Kassiou, Michael and Guilarte, Tomas R and Pomper, Martin G} } @article {818, title = {Reduction of motion-related artifacts in resting state fMRI using aCompCor.}, journal = {Neuroimage}, volume = {96}, year = {2014}, month = {2014 Aug 1}, pages = {22-35}, abstract = {

Recent studies have illustrated that motion-related artifacts remain in resting-state fMRI (rs-fMRI) data even after common corrective processing procedures have been applied, but the extent to which head motion distorts the data may be modulated by the corrective approach taken. We compare two different methods for estimating nuisance signals from tissues not expected to exhibit BOLD fMRI signals of neuronal origin: 1) the more commonly used mean signal method and 2) the principal components analysis approach (aCompCor: Behzadi et al., 2007). Further, we investigate the added benefit of "scrubbing" (Power et al., 2012) following both methods. We demonstrate that the use of aCompCor removes motion artifacts more effectively than tissue-mean signal regression. In addition, inclusion of more components from anatomically defined regions of no interest better mitigates motion-related artifacts and improves the specificity of functional connectivity estimates. While scrubbing further attenuates motion-related artifacts when mean signals are used, scrubbing provides no additional benefit in terms of motion artifact reduction or connectivity specificity when using aCompCor.

}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2014.03.028}, author = {Muschelli, John and Nebel, Mary Beth and Caffo, Brian S and Barber, Anita D and Pekar, James J and Mostofsky, Stewart H} } @article {792, title = {Shrinkage prediction of seed-voxel brain connectivity using resting state fMRI.}, journal = {Neuroimage}, volume = {102 Pt 2}, year = {2014}, month = {2014 Nov 15}, pages = {938-44}, abstract = {

Resting-state functional magnetic resonance imaging (rs-fMRI) is used to investigate synchronous activations in spatially distinct regions of the brain, which are thought to reflect functional systems supporting cognitive processes. Analyses are often performed using seed-based correlation analysis, allowing researchers to explore functional connectivity between data in a seed region and the rest of the brain. Using scan-rescan rs-fMRI data, we investigate how well the subject-specific seed-based correlation map from the second replication of the study can be predicted using data from the first replication. We show that one can dramatically improve prediction of subject-specific connectivity by borrowing strength from the group correlation map computed using all other subjects in the study. Even more surprisingly, we found that the group correlation map provided a better prediction of a subject{\textquoteright}s connectivity than the individual{\textquoteright}s own data. While further discussion and experimentation are required to understand how this can be used in practice, results indicate that shrinkage-based methods that borrow strength from the population mean should play a role in rs-fMRI data analysis.

}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2014.05.043}, author = {Shou, Haochang and Eloyan, Ani and Nebel, Mary Beth and Mejia, Amanda and Pekar, James J and Mostofsky, Stewart and Caffo, Brian and Lindquist, Martin A and Crainiceanu, Ciprian M} } @article {786, title = {Statistical normalization techniques for magnetic resonance imaging.}, journal = {Neuroimage Clin}, volume = {6}, year = {2014}, month = {2014}, pages = {9-19}, abstract = {

While computed tomography and other imaging techniques are measured in absolute units with physical meaning, magnetic resonance images are expressed in arbitrary units that are difficult to interpret and differ between study visits and subjects. Much work in the image processing literature on intensity normalization has focused on histogram matching and other histogram mapping techniques, with little emphasis on normalizing images to have biologically interpretable units. Furthermore, there are no formalized principles or goals for the crucial comparability of image intensities within and across subjects. To address this, we propose a set of criteria necessary for the normalization of images. We further propose simple and robust biologically motivated normalization techniques for multisequence brain imaging that have the same interpretation across acquisitions and satisfy the proposed criteria. We compare the performance of different normalization methods in thousands of images of patients with Alzheimer{\textquoteright}s disease, hundreds of patients with multiple sclerosis, and hundreds of healthy subjects obtained in several different studies at dozens of imaging centers.

}, issn = {2213-1582}, doi = {10.1016/j.nicl.2014.08.008}, author = {Shinohara, Russell T and Sweeney, Elizabeth M and Goldsmith, Jeff and Shiee, Navid and Mateen, Farrah J and Calabresi, Peter A and Jarso, Samson and Pham, Dzung L and Reich, Daniel S and Crainiceanu, Ciprian M} } @article {820, title = {Successful implementation of a unit-based quality nurse to reduce central line-associated bloodstream infections.}, journal = {Am J Infect Control}, volume = {42}, year = {2014}, month = {2014 Feb}, pages = {139-43}, abstract = {

BACKGROUND: Central line (CL)-associated bloodstream infections (CLABSI) are an important cause of patient morbidity and mortality. Novel strategies to prevent CLABSI are needed.

METHODS: We described a quasiexperimental study to examine the effect of the presence of a unit-based quality nurse (UQN) dedicated to perform patient safety and infection control activities with a focus on CLABSI prevention in a surgical intensive care unit (SICU).

RESULTS: From July 2008 to March 2012, there were 3,257 SICU admissions; CL utilization ratio was 0.74 (18,193 CL-days/24,576 patient-days). The UQN program began in July 2010; the nurse was present for 30\% (193/518) of the days of the intervention period of July 2010 to March 2012. The average CLABSI rate was 5.0 per 1,000 CL-days before the intervention and 1.5 after the intervention and decreased by 5.1\% (P = .005) for each additional 1\% of days of the month that the UQN was present, even after adjusting for CLABSI rates in other adult intensive care units, time, severity of illness, and Comprehensive Unit-based Safety Program participation (5.1\%, P = .004). Approximately 11.4 CLABSIs were prevented.

CONCLUSION: The presence of a UQN dedicated to perform infection control activities may be an effective strategy for CLABSI reduction.

}, keywords = {Adult, Catheter-Related Infections, Catheterization, Central Venous, Humans, Infection Control, Intensive Care Units, Nurses, Quality Control, Quality of Health Care}, issn = {1527-3296}, doi = {10.1016/j.ajic.2013.08.006}, author = {Thom, Kerri A and Li, Shanshan and Custer, Melissa and Preas, Michael Anne and Rew, Cindy D and Cafeo, Christina and Leekha, Surbhi and Caffo, Brian S and Scalea, Thomas M and Lissauer, Matthew E} } @article {810, title = {Combining hidden Markov models for comparing the dynamics of multiple sleep electroencephalograms.}, journal = {Stat Med}, volume = {32}, year = {2013}, month = {2013 Aug 30}, pages = {3342-56}, abstract = {

In this manuscript, we consider methods for the analysis of populations of electroencephalogram signals during sleep for the study of sleep disorders using hidden Markov models (HMMs). Notably, we propose an easily implemented method for simultaneously modeling multiple time series that involve large amounts of data. We apply these methods to study sleep-disordered breathing (SDB) in the Sleep Heart Health Study (SHHS), a landmark study of SDB and cardiovascular consequences. We use the entire, longitudinally collected, SHHS cohort to develop HMM population parameters, which we then apply to obtain subject-specific Markovian predictions. From these predictions, we create several indices of interest, such as transition frequencies between latent states. Our HMM analysis of electroencephalogram signals uncovers interesting findings regarding differences in brain activity during sleep between those with and without SDB. These findings include stability of the percent time spent in HMM latent states across matched diseased and non-diseased groups and differences in the rate of transitioning.

}, keywords = {Data Interpretation, Statistical, Electroencephalography, Female, Humans, Longitudinal Studies, Male, Markov Chains, Middle Aged, Models, Statistical, Sleep Apnea Syndromes}, issn = {1097-0258}, doi = {10.1002/sim.5747}, author = {Langrock, Roland and Swihart, Bruce J and Caffo, Brian S and Punjabi, Naresh M and Crainiceanu, Ciprian M} } @article {823, title = {Comparison of total hospital-acquired bloodstream infections to central line-associated bloodstream infections and implications for outcome measures in infection control.}, journal = {Infect Control Hosp Epidemiol}, volume = {34}, year = {2013}, month = {2013 Sep}, pages = {984-6}, abstract = {

The validity of the central line-associated bloodstream infection (CLABSI) measure is compromised by subjectivity. We observed significant decreases in both CLABSIs and total hospital-acquired bloodstream infections (BSIs) following a CLABSI prevention intervention in adult intensive care units. Total hospital-acquired BSIs could be explored as an adjunct, objective CLABSI measure.

}, keywords = {Adult, Catheter-Related Infections, Catheterization, Central Venous, Cross Infection, Humans, Intensive Care Units, Longitudinal Studies, Tertiary Care Centers}, issn = {1559-6834}, doi = {10.1086/671730}, author = {Leekha, Surbhi and Li, Shanshan and Thom, Kerri A and Preas, Michael Anne and Caffo, Brian S and Morgan, Daniel J and Harris, Anthony D} } @article {824, title = {A decision-theory approach to interpretable set analysis for high-dimensional data.}, journal = {Biometrics}, volume = {69}, year = {2013}, month = {2013 Sep}, pages = {614-23}, abstract = {

A key problem in high-dimensional significance analysis is to find pre-defined sets that show enrichment for a statistical signal of interest; the classic example is the enrichment of gene sets for differentially expressed genes. Here, we propose a new decision-theory approach to the analysis of gene sets which focuses on estimating the fraction of non-null variables in a set. We introduce the idea of "atoms," non-overlapping sets based on the original pre-defined set annotations. Our approach focuses on finding the union of atoms that minimizes a weighted average of the number of false discoveries and missed discoveries. We introduce a new false discovery rate for sets, called the atomic false discovery rate (afdr), and prove that the optimal estimator in our decision-theory framework is to threshold the afdr. These results provide a coherent and interpretable framework for the analysis of sets that addresses the key issues of overlapping annotations and difficulty in interpreting p values in both competitive and self-contained tests. We illustrate our method and compare it to a popular existing method using simulated examples, as well as gene-set and brain ROI data analyses.

}, keywords = {Algorithms, Bayes Theorem, Biometry, Brain, Computer Simulation, Data Interpretation, Statistical, Decision Theory, Functional Neuroimaging, Gene Expression Profiling, Genomics, Humans, Magnetic Resonance Imaging, Models, Statistical, Oligonucleotide Array Sequence Analysis}, issn = {1541-0420}, doi = {10.1111/biom.12060}, author = {Boca, Simina M and Bravo, H{\'e}ctor C{\'e}orrada and Caffo, Brian and Leek, Jeffrey T and Parmigiani, Giovanni} } @article {829, title = {Developmental changes in within- and between-network connectivity between late childhood and adulthood.}, journal = {Neuropsychologia}, volume = {51}, year = {2013}, month = {2013 Jan}, pages = {156-67}, abstract = {

A number of behavioral changes occur between late childhood and adulthood, including maturation of social cognition, reward receptivity, impulsiveness, risk-taking and cognitive control. Although some of these abilities show linear improvements with age, some abilities may temporarily worsen, reflecting both the restructuring and/or strengthening of connections within some brain systems. The current study uses resting state functional connectivity to examine developmental differences between late childhood and adulthood in task positive (TP) regions, which play a role in cognitive control functions, and task negative (TN) regions, which play a role in social cognition, self-referential, and internally-directed thought. Within the TP network, developmental differences in connectivity were found with the left dorsolateral prefrontal cortex. Within the TN network, developmental differences in connectivity were found with a broad area of the medial prefrontal cortex and the right parahippocampal gyrus. Connections between the two networks also showed significant developmental differences. Stronger anticorrelations were found in the TN maps of the adult group for the right anterior insula/inferior frontal gyrus, bilateral anterior inferior parietal lobule, bilateral superior parietal lobule and an anterior portion of the right posterior cingulate cortex. There was a significant brain-behavior relationship between the strength of anticorrelation in these regions and inhibitory control performance on two Go/No-go tasks suggesting that the development of anticorrelations between late childhood and adulthood supports mature inhibitory control. Overall, maturation of these networks occurred in specific regions which are associated with cognitive control of goal-directed behavior, including those involved in working memory, social cognition, and inhibitory control.

}, keywords = {Adolescent, Adult, Age Factors, Analysis of Variance, Brain, brain mapping, Child, Child Development, Cognition, Female, Humans, Image Processing, Computer-Assisted, Inhibition (Psychology), Magnetic Resonance Imaging, Male, Middle Aged, Neural Pathways, Neuropsychological Tests, Oxygen, Reaction Time, Young Adult}, issn = {1873-3514}, doi = {10.1016/j.neuropsychologia.2012.11.011}, author = {Barber, Anita D and Caffo, Brian S and Pekar, James J and Mostofsky, Stewart H} } @article {826, title = {Effects of working memory demand on neural mechanisms of motor response selection and control.}, journal = {J Cogn Neurosci}, volume = {25}, year = {2013}, month = {2013 Aug}, pages = {1235-48}, abstract = {

Inhibitory control commonly recruits a number of frontal regions: pre-supplementary motor area (pre-SMA), frontal eye fields (FEFs), and right-lateralized posterior inferior frontal gyrus (IFG), dorsal anterior insula (DAI), dorsolateral prefrontal cortex (DLPFC), and inferior frontal junction (IFJ). These regions may directly implement inhibitory motor control or may be more generally involved in executive control functions. Two go/no-go tasks were used to distinguish regions specifically recruited for inhibition from those that additionally show increased activity with working memory demand. The pre-SMA and IFG were recruited for inhibition in both tasks and did not have greater activation for working memory demand on no-go trials, consistent with a role in inhibitory control. Activation in pre-SMA also responded to response selection demand and was increased with working memory on go trials specifically. The bilateral FEF and right DAI were commonly active for no-go trials. The FEF was also recruited to a greater degree with working memory demand on go trials and may bias top-down information when stimulus-response mappings change. The DAI, additionally responded to increased working memory demand on both go and no-go trials and may be involved in accessing sustained task information, alerting, or autonomic changes when cognitive demands increase. DLPFC activation was consistent with a role in working memory retrieval on both go and no-go trials. The inferior frontal junction, on the other hand, had greater activation with working memory specifically for no-go trials and may detect salient stimuli when the task requires frequent updating of working memory representations.

}, keywords = {Adult, Brain, brain mapping, Choice Behavior, Female, Humans, Image Processing, Computer-Assisted, Inhibition (Psychology), Magnetic Resonance Imaging, Male, Memory, Short-Term, Motor Activity, Neuropsychological Tests, Oxygen, Reaction Time, Young Adult}, issn = {1530-8898}, doi = {10.1162/jocn_a_00394}, author = {Barber, Anita D and Caffo, Brian S and Pekar, James J and Mostofsky, Stewart H} } @article {802, title = {OASIS is Automated Statistical Inference for Segmentation, with applications to multiple sclerosis lesion segmentation in MRI.}, journal = {Neuroimage Clin}, volume = {2}, year = {2013}, month = {2013}, pages = {402-13}, abstract = {

Magnetic resonance imaging (MRI) can be used to detect lesions in the brains of multiple sclerosis (MS) patients and is essential for diagnosing the disease and monitoring its progression. In practice, lesion load is often quantified by either manual or semi-automated segmentation of MRI, which is time-consuming, costly, and associated with large inter- and intra-observer variability. We propose OASIS is Automated Statistical Inference for Segmentation (OASIS), an automated statistical method for segmenting MS lesions in MRI studies. We use logistic regression models incorporating multiple MRI modalities to estimate voxel-level probabilities of lesion presence. Intensity-normalized T1-weighted, T2-weighted, fluid-attenuated inversion recovery and proton density volumes from 131 MRI studies (98 MS subjects, 33 healthy subjects) with manual lesion segmentations were used to train and validate our model. Within this set, OASIS detected lesions with a partial area under the receiver operating characteristic curve for clinically relevant false positive rates of 1\% and below of 0.59\% (95\% CI; [0.50\%, 0.67\%]) at the voxel level. An experienced MS neuroradiologist compared these segmentations to those produced by LesionTOADS, an image segmentation software that provides segmentation of both lesions and normal brain structures. For lesions, OASIS out-performed LesionTOADS in 74\% (95\% CI: [65\%, 82\%]) of cases for the 98 MS subjects. To further validate the method, we applied OASIS to 169 MRI studies acquired at a separate center. The neuroradiologist again compared the OASIS segmentations to those from LesionTOADS. For lesions, OASIS ranked higher than LesionTOADS in 77\% (95\% CI: [71\%, 83\%]) of cases. For a randomly selected subset of 50 of these studies, one additional radiologist and one neurologist also scored the images. Within this set, the neuroradiologist ranked OASIS higher than LesionTOADS in 76\% (95\% CI: [64\%, 88\%]) of cases, the neurologist 66\% (95\% CI: [52\%, 78\%]) and the radiologist 52\% (95\% CI: [38\%, 66\%]). OASIS obtains the estimated probability for each voxel to be part of a lesion by weighting each imaging modality with coefficient weights. These coefficients are explicit, obtained using standard model fitting techniques, and can be reused in other imaging studies. This fully automated method allows sensitive and specific detection of lesion presence and may be rapidly applied to large collections of images.

}, issn = {2213-1582}, doi = {10.1016/j.nicl.2013.03.002}, author = {Sweeney, Elizabeth M and Shinohara, Russell T and Shiee, Navid and Mateen, Farrah J and Chudgar, Avni A and Cuzzocreo, Jennifer L and Calabresi, Peter A and Pham, Dzung L and Reich, Daniel S and Crainiceanu, Ciprian M} } @article {811, title = {Relationships between retinal axonal and neuronal measures and global central nervous system pathology in multiple sclerosis.}, journal = {JAMA Neurol}, volume = {70}, year = {2013}, month = {2013 Jan}, pages = {34-43}, abstract = {

OBJECTIVE: To determine the relationships between conventional and segmentation-derived optical coherence tomography (OCT) retinal layer thickness measures with intracranial volume (a surrogate of head size) and brain substructure volumes in multiple sclerosis (MS).

DESIGN: Cross-sectional study.

SETTING: Johns Hopkins University, Baltimore, Maryland.

PARTICIPANTS: A total of 84 patients with MS and 24 healthy control subjects.

MAIN OUTCOME MEASURES: High-definition spectral-domain OCT conventional and automated segmentation-derived discrete retinal layer thicknesses and 3-T magnetic resonance imaging brain substructure volumes.

RESULTS: Peripapillary retinal nerve fiber layer as well as composite ganglion cell layer+inner plexiform layer thicknesses in the eyes of patients with MS without a history of optic neuritis were associated with cortical gray matter (P=.01 and P=.04, respectively) and caudate (P=.04 and P=.03, respectively) volumes. Inner nuclear layer thickness, also in eyes without a history of optic neuritis, was associated with fluid-attenuated inversion recovery lesion volume (P=.007) and inversely associated with normal-appearing white matter volume (P=.005) in relapsing-remitting MS. As intracranial volume was found to be related with several of the OCT measures in patients with MS and healthy control subjects and is already known to be associated with brain substructure volumes, all OCT-brain substructure relationships were adjusted for intracranial volume. CONCLUSIONS Retinal measures reflect global central nervous system pathology in multiple sclerosis, with thicknesses of discrete retinal layers each appearing to be associated with distinct central nervous system processes. Moreover, OCT measures appear to correlate with intracranial volume in patients with MS and healthy control subjects, an important unexpected factor unaccounted for in prior studies examining the relationships between peripapillary retinal nerve fiber layer thickness and brain substructure volumes.

}, keywords = {Adult, Axons, Caudate Nucleus, Central Nervous System, Cerebral Cortex, Cross-Sectional Studies, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Multiple Sclerosis, Retina, Retinal Neurons, Tomography, Optical Coherence}, issn = {2168-6157}, doi = {10.1001/jamaneurol.2013.573}, author = {Saidha, Shiv and Sotirchos, Elias S and Oh, Jiwon and Syc, Stephanie B and Seigo, Michaela A and Shiee, Navid and Eckstein, Chistopher and Durbin, Mary K and Oakley, Jonathan D and Meyer, Scott A and Frohman, Teresa C and Newsome, Scott and Ratchford, John N and Balcer, Laura J and Pham, Dzung L and Crainiceanu, Ciprian M and Frohman, Elliot M and Reich, Daniel S and Calabresi, Peter A} } @article {827, title = {Analysis of group ICA-based connectivity measures from fMRI: application to Alzheimer{\textquoteright}s disease.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e49340}, abstract = {

Functional magnetic resonance imaging (fMRI) is a powerful tool for the in vivo study of the pathophysiology of brain disorders and disease. In this manuscript, we propose an analysis stream for fMRI functional connectivity data and apply it to a novel study of Alzheimer{\textquoteright}s disease. In the first stage, spatial independent component analysis is applied to group fMRI data to obtain common brain networks (spatial maps) and subject-specific mixing matrices (time courses). In the second stage, functional principal component analysis is utilized to decompose the mixing matrices into population-level eigenvectors and subject-specific loadings. Inference is performed using permutation-based exact logistic regression for matched pairs data. The method is applied to a novel fMRI study of Alzheimer{\textquoteright}s disease risk under a verbal paired associates task. We found empirical evidence of alternative ICA-based metrics of connectivity when comparing subjects evidencing mild cognitive impairment relative to carefully matched controls.

}, keywords = {Aged, Algorithms, Alzheimer Disease, Brain, brain mapping, Case-Control Studies, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Mild Cognitive Impairment, Nerve Net, Principal Component Analysis, Task Performance and Analysis, Time Factors}, issn = {1932-6203}, doi = {10.1371/journal.pone.0049340}, author = {Li, Shanshan and Eloyan, Ani and Joel, Suresh and Mostofsky, Stewart and Pekar, James and Bassett, Susan Spear and Caffo, Brian} } @article {685, title = {Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling.}, journal = {BMC Bioinformatics}, volume = {13}, year = {2012}, month = {2012 Sep 14}, pages = {234}, abstract = {

ABSTRACT: BACKGROUND: Existing statistical methods for tiling array transcriptome data either focus on transcript discovery in one biological or experimental condition or on the detection of differential expression between two conditions. Increasingly often, however, biologists are interested in time-course studies, studies with more than two conditions or even multiple-factor studies. As these studies are currently analyzed with the traditional microarray analysis techniques, they do not exploit the genome-wide nature of tiling array data to its full potential. RESULTS: We present an R Bioconductor package, waveTiling, which implements a wavelet-based model for analyzing transcriptome data and extends it towards more complex experimental designs. With waveTiling the user is able to discover (1) group-wise expressed regions, (2) differentially expressed regions between any two groups in single-factor studies and in (3) multifactorial designs. Moreover, for time-course experiments it is also possible to detect (4) linear time effects and (5) a circadian rhythm of transcripts. By considering the expression values of the individual tiling probes as a function of genomic position, effect regions can be detected regardless of existing annotation. Three case studies with different experimental set-ups illustrate the use and the flexibility of the model-based transcriptome analysis. CONCLUSIONS: The waveTiling package provides the user with a convenient tool for the analysis of tiling array trancriptome data for a multitude of experimental set-ups. Regardless of the study design, the probe-wise analysis allows for the detection of transcriptional effects in both exonic, intronic and intergenic regions, without prior consultation of existing annotation.

}, issn = {1471-2105}, doi = {10.1186/1471-2105-13-234}, author = {De Beuf, K. and Pipelers, Peter and Andriankaja, Megan and Thas, O. and Inz{\'e}, Dirk and Crainiceanu, C and Clement, Lieven} } @article {679, title = {Bootstrap-based inference on the difference in the means of two correlated functional processes.}, journal = {Stat Med}, year = {2012}, month = {2012 Aug 1}, abstract = {

We propose nonparametric inference methods on the mean difference between two correlated functional processes. We compare methods that (1) incorporate different levels of smoothing of the mean and covariance; (2) preserve the sampling design; and (3) use parametric and nonparametric estimation of the mean functions. We apply our method to estimating the mean difference between average normalized δ power of sleep electroencephalograms for 51 subjects with severe sleep apnea and 51 matched controls in the first 4\ ;h after sleep onset. We obtain data from the Sleep Heart Health Study, the largest community cohort study of sleep. Although methods are applied to a single case study, they can be applied to a large number of studies that have correlated functional data. Copyright {\textcopyright} 2012 John Wiley \& Sons, Ltd.

}, issn = {1097-0258}, doi = {10.1002/sim.5439}, author = {Crainiceanu, C and Staicu, A. M. and Ray, Shubankar and Punjabi, Naresh} } @article {pmid22472185, title = {Cadmium Exposure and All Cause and Cardiovascular Mortality in the US General Population}, journal = {Environ Health Perspect}, year = {2012}, month = {Apr}, author = {Tellez-Plaza, M. and Navas-Acien, A. and Menke, A. and Crainiceanu, C and Pastor-Barriuso, R. and Guallar, E.} } @article {pmid22221585, title = {Effect of correcting for long-term variation in major coronary heart disease risk factors: relative hazard estimation and risk prediction in the Atherosclerosis Risk in Communities Study}, journal = {Ann Epidemiol}, volume = {22}, number = {3}, year = {2012}, month = {Mar}, pages = {191{\textendash}197}, author = {Paynter, N. P. and Crainiceanu, C and Sharrett, A. R. and Chambless, L. E. and Coresh, J.} } @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 {reiss2012paradox, title = {Paradoxical Results of Adaptive False Discovery Rate Procedures in Neuroimaging Studies}, journal = {NeuroImage}, year = {2012}, note = {To appear}, author = {Philip T. Reiss, Armin Schwartzman, Feihan Lu, Lei Huang, and Erika Proal} } @article {710, title = {Relationships Between Retinal Axonal and Neuronal Measures and Global Central Nervous System Pathology in Multiple Sclerosis.}, journal = {Arch Neurol}, year = {2012}, month = {2012 Oct 1}, pages = {1-10}, abstract = {

OBJECTIVE To determine the relationships between conventional and segmentation-derived optical coherence tomography (OCT) retinal layer thickness measures with intracranial volume (a surrogate of head size) and brain substructure volumes in multiple sclerosis (MS). DESIGN Cross-sectional study. SETTING Johns Hopkins University, Baltimore, Maryland. PARTICIPANTS A total of 84 patients with MS and 24 healthy control subjects. MAIN OUTCOME MEASURES High-definition spectral-domain OCT conventional and automated segmentation-derived discrete retinal layer thicknesses and 3-T magnetic resonance imaging brain substructure volumes. RESULTS Peripapillary retinal nerve fiber layer as well as composite ganglion cell layer\ +\ inner plexiform layer thicknesses in the eyes of patients with MS without a history of optic neuritis were associated with cortical gray matter (P\ =\ .01 and P\ =\ .04, respectively) and caudate (P\ =\ .04 and P\ =\ .03, respectively) volumes. Inner nuclear layer thickness, also in eyes without a history of optic neuritis, was associated with fluid-attenuated inversion recovery lesion volume (P\ =\ .007) and inversely associated with normal-appearing white matter volume (P\ =\ .005) in relapsing-remitting MS. As intracranial volume was found to be related with several of the OCT measures in patients with MS and healthy control subjects and is already known to be associated with brain substructure volumes, all OCT-brain substructure relationships were adjusted for intracranial volume. CONCLUSIONS Retinal measures reflect global central nervous system pathology in multiple sclerosis, with thicknesses of discrete retinal layers each appearing to be associated with distinct central nervous system processes. Moreover, OCT measures appear to correlate with intracranial volume in patients with MS and healthy control subjects, an important unexpected factor unaccounted for in prior studies examining the relationships between peripapillary retinal nerve fiber layer thickness and brain substructure volumes.

}, issn = {1538-3687}, doi = {10.1001/archneurol.2013.573}, author = {Saidha, Shiv and Sotirchos, Elias S and Oh, Jiwon and Syc, Stephanie B and Seigo, Michaela A and Shiee, Navid and Eckstein, Chistopher and Durbin, Mary K and Oakley, Jonathan D and Meyer, Scott A and Frohman, Teresa C and Newsome, Scott and Ratchford, John N and Balcer, Laura J and Pham, Dzung L and Crainiceanu, Ciprian M and Frohman, Elliot M and Reich, Daniel S and Calabresi, Peter A} } @article {abikoff2012quantile, title = {Remediating Organizational Functioning in Children with ADHD: Immediate and Long- Term Effects from a Randomized Controlled Trial}, journal = {Journal of Consulting and Clinical Psychology}, year = {2012}, note = {In Press}, author = {Howard Abikoff, Richard Gallagher, Karen C. Wells, Desiree W. Murray, Lei Huang, Feihan Lu, and Petkova, E.} } @article {shee, title = {Revisiting Brain Atrophy and Its Relationship to Disability in Multiple Sclerosis}, journal = {PLoS ONE}, volume = {7}, number = {5}, year = {2012}, month = {05}, pages = {e37049}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0037049}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0037049}, author = {Shiee, N and Bazin, P and Zackowski, K and Farrell, S and Harrison, D and Newsome, S and Ratchford, J and Caffo, B and Calabresi, P and Pham, D and Reich, D.} } @article {nareshCaffeine, title = {Sleep-Disordered breathing and caffeine consumption: results of a community-based study}, journal = {Accepted in Chest}, year = {2012}, author = {Aurora, RN and Crainiceanu, C and Caffo, B and Punjabi, N} } @article {830, title = {Total white matter hyperintensity volume in bipolar disorder patients and their healthy relatives.}, journal = {Bipolar Disord}, volume = {14}, year = {2012}, month = {2012 Dec}, pages = {888-93}, abstract = {

OBJECTIVES: White matter hyperintensities (WMH) are more common in subjects with bipolar disorder (BP) than in healthy subjects (HS). Few studies have examined the effect of the diagnostic type of bipolar illness on WMH burden, and none have approached this question through a direct measurement of the volume of affected white matter in relationship to familiality. In this pilot study, we utilized a volumetric measurement of WMH to investigate the relationship between the total volume of WMH and the familiality and type of BP.

METHODS: Forty-five individuals with bipolar I disorder (BP-I) with psychotic features, BP-I without psychotic features, or bipolar II disorder (BP-II), seven of their unaffected relatives, and 32 HS were recruited for participation. T-2 weighted magnetic resonance imaging scans were obtained on all subjects, and the total volume of all WMH for each subject was measured in cubic centimeters. The significance of difference between groups was tested using ANOVA with post-hoc adjustment for multiple comparisons. Further, we used logistic regression to test for trends between symptom load and total WMH volume.

RESULTS: The mean total volume of WMH in BP-I patients with psychotic features was significantly higher (p < 0.05) than that of HS. Further, we observed a positive linear trend by familiality and type of affectedness when comparing mean total WMH volume of HS, unaffected family members, subjects with BP-II, and BP-I with and without a history of psychosis (p < 0.05).

CONCLUSIONS: Based on a quantitative technique, WMH burden appears to be associated with familiality and type of BP. The significance of these findings remains to be fully elucidated.

}, keywords = {Adult, Analysis of Variance, Bipolar Disorder, Brain, Female, Humans, Image Processing, Computer-Assisted, Leukoencephalopathies, Magnetic Resonance Imaging, Male, Nerve Fibers, Myelinated}, issn = {1399-5618}, doi = {10.1111/bdi.12019}, author = {Tighe, Sarah K and Reading, Sarah A and Rivkin, Paul and Caffo, Brian and Schweizer, Barbara and Pearlson, Godfrey and Potash, James B and Depaulo, J Raymond and Bassett, Susan S} } @article {springerlink:10.1007/s10928-011-9211-7, title = {A Bayesian hierarchical nonlinear mixture model in the presence of artifactual outliers in a population pharmacokinetic study}, journal = {Journal of Pharmacokinetics and Pharmacodynamics}, volume = {38}, year = {2011}, note = {10.1007/s10928-011-9211-7}, pages = {613-636}, publisher = {Springer Netherlands}, issn = {1567-567X}, url = {http://dx.doi.org/10.1007/s10928-011-9211-7}, author = {Choi, L and Caffo, B and Kohli, U and Pandharipande, P and Kurnik, D and Ely, E and Stein, C} } @article {aurora2011correlating, title = {Correlating subjective and objective sleepiness: revisiting the association using survival analysis.}, journal = {Sleep}, volume = {34}, number = {12}, year = {2011}, pages = {1707}, author = {Aurora, RN and Caffo, B and Crainiceanu, C and Punjabi, N} } @article {reiss2011extracting, title = {Extracting information from functional connectivity maps via function-on-scalar regression}, journal = {NeuroImage}, volume = {56}, number = {1}, year = {2011}, pages = {140{\textendash}148}, author = {Reiss, P.T. and Mennes, M. and Petkova, E. and Huang, L. and Hoptman, M.J. and Biswal, B.B. and Colcombe, S.J. and Zuo, X.N. and Milham, M.P.} } @article {VP11_QAP, title = {Fast Inexact Graph Mathing with Applications in Statistical Connectomics}, journal = {under review}, year = {2011}, author = {Vogelstein, Joshua T and Conroy, John C and Podrazik, Louis J and Kratzer, Steven G and Fishkind, Donniell E and Vogelstein, Joshua T and Priebe, Carey E} } @article {VP11_sigsub, title = {Graph Classification using Signal Subgraphs: Applications in Statistical Connectomics}, journal = {under review}, year = {2011}, author = {Vogelstein, Joshua T and Gray, William R and Vogelstein, Joshua T and Priebe, Carey E} } @article {Yuste2011, title = {Imaging action potentials with calcium indicators.}, journal = {Cold Spring Harbor protocols}, volume = {2009}, number = {8}, year = {2011}, pages = {pdb.prot5316}, abstract = {

The understanding of neuronal circuits has been, and will continue to be, greatly advanced by the simultaneous imaging of action potentials in neuronal ensembles. This protocol describes "bulk" loading of brain slices with acetoxymethyl (AM) ester calcium indicators in order to monitor action potential activity in large populations of neurons simultaneously. The imaging of calcium influx into neurons provides an indirect, but accurate, measure of action potential generation in individual neurons. Single-cell resolution, and thus the easy identification of every active cell, is the key advantage of the technique.

}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21807854}, author = {Yuste, Rafael and MacLean, Jason and Vogelstein, Joshua T and Paninski, Liam} } @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 {caffoSleep, title = {A novel approach to prediction of mild sleep disorders in a population-based sample: the Sleep Heart Health Study}, journal = {Sleep, PMCID: PMC2982734}, volume = {33}, number = {12}, year = {2011}, pages = {1641{\textendash}1648}, author = {Caffo, B and Diener-West, M and Punjabi, N and Samet, J} } @article {doi:10.1198/jasa.2011.ap10089, title = {Population value decomposition, a framework for the analysis of image populations}, journal = {Journal of the American Statistical Association, with discussion and rejoinder}, volume = {106}, number = {495}, year = {2011}, pages = {775-790}, doi = {10.1198/jasa.2011.ap10089}, url = {http://pubs.amstat.org/doi/abs/10.1198/jasa.2011.ap10089}, author = {Crainiceanu, C and Caffo, B and Luo, S and Zipunnikov, V. and Punjabi, N} } @article {MRM:MRM22818, title = {On the relationship between seed-based and ICA-based measures of functional connectivity}, journal = {Magnetic Resonance in Medicine}, volume = {66}, number = {3}, year = {2011}, pages = {644{\textendash}657}, publisher = {Wiley Subscription Services, Inc., A Wiley Company}, keywords = {between network connectivity, blood oxygenation level dependent fMRI, functional connectivity, ICA, seed-based connectivity, within network connectivity}, issn = {1522-2594}, doi = {10.1002/mrm.22818}, url = {http://dx.doi.org/10.1002/mrm.22818}, author = {Joel, S. and Caffo, B and van Zijl, P and Pekar, J} } @article {VP11_unlabeled, title = {Shuffled Graph Classification: Theory and Connectome Applications}, journal = {under review}, year = {2011}, author = {Vogelstein, Joshua T and Priebe, Carey E} } @article {kriegeskorte2010everything, title = {Everything you never wanted to know about circular analysis, but were afraid to ask}, journal = {Journal of Cerebral Blood Flow \& Metabolism}, volume = {30}, number = {9}, year = {2010}, pages = {1551{\textendash}1557}, publisher = {Nature Publishing Group}, author = {Kriegeskorte, Nikolaus and Lindquist, Martin A and Nichols, Thomas E and Poldrack, Russell A and Vul, Edward} } @article {847, title = {Everything you never wanted to know about circular analysis, but were afraid to ask.}, journal = {J Cereb Blood Flow Metab}, volume = {30}, year = {2010}, month = {2010 Sep}, pages = {1551-7}, abstract = {

Over the past year, a heated discussion about {\textquoteright}circular{\textquoteright} or {\textquoteright}nonindependent{\textquoteright} analysis in brain imaging has emerged in the literature. An analysis is circular (or nonindependent) if it is based on data that were selected for showing the effect of interest or a related effect. The authors of this paper are researchers who have contributed to the discussion and span a range of viewpoints. To clarify points of agreement and disagreement in the community, we collaboratively assembled a series of questions on circularity herein, to which we provide our individual current answers in }, keywords = {Brain, brain mapping, Data Interpretation, Statistical, Guidelines as Topic, Image Processing, Computer-Assisted, Neurosciences, Publications, Research Design, Selection Bias}, issn = {1559-7016}, doi = {10.1038/jcbfm.2010.86}, author = {Kriegeskorte, Nikolaus and Lindquist, Martin A and Nichols, Thomas E and Poldrack, Russell A and Vul, Edward} } @article {swihart2009lasagna, title = {Lasagna plots: A Saucy alternative to spaghetti plots}, journal = {Epidemiology}, volume = {21}, number = {5}, year = {2010}, pages = {621{\textendash}625}, author = {Swihart, B and Caffo, B and James, B and Strand, M. and Schwartz, B and Punjabi, N} } @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 {Paninski2010, title = {A new look at state-space models for neural data.}, journal = {Journal of computational neuroscience}, volume = {29}, number = {1-2}, year = {2010}, pages = {107{\textendash}26}, abstract = {

State space methods have proven indispensable in neural data analysis. However, common methods for performing inference in state-space models with non-Gaussian observations rely on certain approximations which are not always accurate. Here we review direct optimization methods that avoid these approximations, but that nonetheless retain the computational efficiency of the approximate methods. We discuss a variety of examples, applying these direct optimization techniques to problems in spike train smoothing, stimulus decoding, parameter estimation, and inference of synaptic properties. Along the way, we point out connections to some related standard statistical methods, including spline smoothing and isotonic regression. Finally, we note that the computational methods reviewed here do not in fact depend on the state-space setting at all; instead, the key property we are exploiting involves the bandedness of certain matrices. We close by discussing some applications of this more general point of view, including Markov chain Monte Carlo methods for neural decoding and efficient estimation of spatially-varying firing rates.

}, keywords = {1 introduction, Action Potentials, Action Potentials: physiology, Animals, Computer Simulation, for inference in state-space, forward-backward methods, hidden markov model, models, neural coding, Neurological, Neurons, Neurons: physiology, Retinal Ganglion Cells, Retinal Ganglion Cells: physiology, state-space models, Statistical, Synapses, Synapses: physiology, tridiagonal matrix}, issn = {1573-6873}, doi = {10.1007/s10827-009-0179-x}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19649698}, author = {Paninski, Liam and Ahmadian, Yashar and Gil, Daniel and Shinsuke, Ferreira and Rahnama, Kamiar and Michael, Rad and Vogelstein, Joshua T and Wu, Wei and Ferreira, Daniel Gil and Koyama, Shinsuke and {Rahnama Rad}, Kamiar and Vidne, Michael} } @article {pmid20227508, title = {Two-stage decompositions for the analysis of functional connectivity for fMRI with application to Alzheimer{\textquoteright}s disease risk}, journal = {Neuroimage}, volume = {51}, number = {3}, year = {2010}, month = {Jul}, pages = {1140{\textendash}1149}, author = {Caffo, B and Crainiceanu, C and Verduzco, G. and Joel, S. and Mostofsky, S and Bassett, S and Pekar, J} } @article {laffan2010utility, title = {Utility of sleep stage transitions in assessing sleep continuity}, journal = {Sleep, PMCID: PMC2982738}, volume = {33}, number = {12}, year = {2010}, pages = {1681}, issn = {0161-8105}, author = {Laffan, A and Caffo, B and Swihart, B and Punjabi, N} } @article {MishchenkoPaninski09, title = {A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data}, journal = {Annals of Applied Statistics}, volume = {in press}, year = {2009}, author = {Mishchenko, Yuriy and Vogelstein, Joshua T and Paninski, Liam} } @article {mostofsky2009decreased, title = {Decreased connectivity and cerebellar activity in autism during motor task performance}, journal = {Brain, PMCID: PMC2732264}, volume = {132}, number = {9}, year = {2009}, pages = {2413{\textendash}2425}, publisher = {Oxford Univ Press}, author = {Mostofsky, S and Powell, S and Simmonds, D and Goldberg, M and Caffo, B and Pekar, J} } @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 {crainiceanu2009nonparametric, title = {Nonparametric signal extraction and measurement error in the analysis of electroencephalographic activity during sleep}, journal = {Journal of the American Statistical Association, PMCID: PMC2802498}, volume = {104}, number = {486}, year = {2009}, pages = {541{\textendash}555}, publisher = {ASA}, author = {Crainiceanu, C and Caffo, B and Di, C and Punjabi, N} } @article {Crai:Caff:Di:Punj:nonp:2009, title = {Nonparametric Signal Extraction and Measurement Error in the Analysis of Electroencephalographic Activity During Sleep}, journal = {Journal of the American Statistical Association}, volume = {104}, number = {486}, year = {2009}, pages = {541{\textendash}555}, keywords = {Hierarchical smoothing, Measurement error, penalized splines, Sleep}, author = {Crainiceanu, C and Caffo, B and Di, Chong-Zhi and Punjabi, Naresh M} } @article {caffo2009overview, title = {An overview of observational sleep research with application to sleep stage transitioning}, journal = {Chance, PMCID: PMC2800358}, volume = {22}, number = {1}, year = {2009}, pages = {10{\textendash}15}, publisher = {Springer}, author = {Caffo, B and Swihart, B and Crainiceanu, C and Laffan, A and Punjabi, N} } @article {Caff:Swih:Crai:Laff:Punj:an:2009, title = {An Overview of Observational Sleep Research with Application to Sleep State Transitioning}, journal = {Chance}, volume = {22}, number = {1}, year = {2009}, pages = {10{\textendash}15}, author = {Caffo, B and Swihart, B and Crainiceanu, C and Laffan, A and Punjabi, Naresh} } @article {punjabi, title = {Sleep-disordered Breathing and Mortality: a Prospective Cohort Study}, journal = {PLOS Medicine, PMCID: PMC2722083}, volume = {6}, year = {2009}, author = {Punjabi, N and Caffo, B and Goodwin, J and Gottlieb, D and Newman, A and O{\textquoteright}Connor, G and Rapoport, D and Redline, S and Resnick, H and Robbins, J and Samet, J and Shahar, E and Unruh, M} } @article {VogelsteinPaninski09, title = {Spike inference from calcium imaging using sequential Monte Carlo methods.}, journal = {Biophys J}, volume = {97}, number = {2}, year = {2009}, pages = {636{\textendash}655}, publisher = {Department of Neuroscience, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA. joshuav@jhu.edu}, abstract = {

As recent advances in calcium sensing technologies facilitate simultaneously imaging action potentials in neuronal populations, complementary analytical tools must also be developed to maximize the utility of this experimental paradigm. Although the observations here are fluorescence movies, the signals of interest{\textendash}spike trains and/or time varying intracellular calcium concentrations{\textendash}are hidden. Inferring these hidden signals is often problematic due to noise, nonlinearities, slow imaging rate, and unknown biophysical parameters. We overcome these difficulties by developing sequential Monte Carlo methods (particle filters) based on biophysical models of spiking, calcium dynamics, and fluorescence. We show that even in simple cases, the particle filters outperform the optimal linear (i.e., Wiener) filter, both by obtaining better estimates and by providing error bars. We then relax a number of our model assumptions to incorporate nonlinear saturation of the fluorescence signal, as well external stimulus and spike history dependence (e.g., refractoriness) of the spike trains. Using both simulations and in vitro fluorescence observations, we demonstrate temporal superresolution by inferring when within a frame each spike occurs. Furthermore, the model parameters may be estimated using expectation maximization with only a very limited amount of data (e.g., approximately 5-10 s or 5-40 spikes), without the requirement of any simultaneous electrophysiology or imaging experiments.

}, keywords = {Animals, Biological, Calcium, cytology/metabolism, Fluorescence, Inbred C57BL, Intracellular Space, metabolism, Mice, models, Monte Carlo Method, Neurons, Probability, Time Factors}, doi = {10.1016/j.bpj.2008.08.005}, url = {http://dx.doi.org/10.1016/j.bpj.2008.08.005}, author = {Vogelstein, Joshua T and Watson, Brendon O and Packer, Adam M and Yuste, Rafael and Jedynak, Bruno and Paninski, Liam} } @article {Crai:Domi:adju:2008, title = {Adjustment Uncertainty in Effect Estimation}, journal = {Biometrika}, volume = {95}, number = {3}, year = {2008}, pages = {635{\textendash}651}, keywords = {Air pollution, Bayesian model averaging}, author = {Crainiceanu, C and Dominici, Francesca and Parmigiani, G.} } @article {swihart2008quantitative, title = {Characterizing Sleep Structure Using the Hypnogram}, journal = {Journal of Clinical Sleep Medicine, PMCID: PMC2542492}, volume = {4}, number = {4}, year = {2008}, pages = {349{\textendash}355}, author = {Swihart, B and Caffo, B and Bandeen-Roche, K and Punjabi, N} } @article {redgrave2008differential, title = {Differential brain activation in anorexia nervosa to Fat and Thin words during a Stroop task}, journal = {NeuroReport, PMCID: PMC2891098}, volume = {19}, number = {12}, year = {2008}, pages = {1181{\textendash}1185}, author = {Redgrave, G and Bakker, A and Bello, N and Caffo, B and Coughlin, J and Guarda, A and McEntee, J and Pekar, J and Reinblatt, S and Verduzco, G. and Moran, T} } @article {guilarte2008dysregulation, title = {Dysregulation of Glutamate Carboxypeptidase II in Psychiatric Disease}, journal = {Schizophrenia Research, PMCID: PMC2287371}, volume = {99}, number = {1-3}, year = {2008}, pages = {324{\textendash}332}, publisher = {NIH Public Access}, author = {Guilarte, T and Hammoud, D and McGlothan, J and Caffo, B and Foss, C and Kozikowski, A and Pomper, M} } @article {stamatakis2008fasting, title = {Fasting Glycemia in Sleep Disordered Breathing: Lowering the Threshold on Oxyhemoglobin Desaturation}, journal = {Sleep, PMCID: PMC2491502}, volume = {31}, number = {7}, year = {2008}, pages = {1018{\textendash}1024}, publisher = {American Academy of Sleep Medicine}, author = {Stamatakis, K and Sanders, M and Caffo, B and Resnick, H and Gottlieb, D and Mehra, R and Punjabi, N} } @article {suskauer2008fmri, title = {fMRI of Intrasubject Variability in ADHD: Anomalous Premotor Activity With Prefrontal Compensation}, journal = {Journal of American Academy of Child \& Adolescent Psychiatry, NIHMSID: 71813}, volume = {47}, number = {10}, year = {2008}, pages = {1141{\textendash}1150}, author = {Suskauer, S and Simmonds, D and Caffo, B and Denckla, M and Pekar, J and Mostofsky, S} } @article {caffo2008likelihood, title = {Likelihood Estimation of Conjugacy Relationships in Linear Models with Applications to High-Throughput Genomics}, journal = {International Journal of Biostatistics, PMCID: PMC2827886}, volume = {5}, year = {2008}, note = {Issue 18}, publisher = {bepress}, author = {Caffo, B and Dongmei, L and Scharpf, R and Parmigiani, G.} } @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 {zhang2008power, title = {Power Spectral Analysis of EEG Activity During Sleep in Cigarette Smokers}, journal = {Chest}, volume = {133}, number = {2}, year = {2008}, pages = {427{\textendash}432}, publisher = {Am Coll Chest Phys}, author = {Zhang, L and Samet, J and Caffo, B and Bankman, I and Punjabi, N} } @article {Grev:Crai:Kche:Pete:rest:2008, title = {Restricted Likelihood Ratio Testing for Zero Variance Components in Linear Mixed Models}, journal = {Journal of Computational and Graphical Statistics}, volume = {17}, number = {4}, year = {2008}, pages = {870{\textendash}891}, keywords = {Nonparametric 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