Towards structured sharing of raw and derived neuroimaging data across existing resources

Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary for making use of the combined, available neuroimaging data. In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating Facility (INCF) focused on practical tools for distributed access to neuroimaging data. The working group develops models and tools facilitating the structured interchange of neuroimaging meta-data and is making progress towards a unified set of tools for such data and meta-data exchange. We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources. The components include (1) a structured terminology that provides semantic context to data, (2) a formal data model for neuroimaging with robust tracking of data provenance, (3) a web service-based application programming interface (API) that provides a consistent mechanism to access and query the data model, and (4) a provenance library that can be used for the extraction of provenance data by image analysts and imaging software developers. We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging data across the various existing database systems for the purpose of accelerating scientific discovery

The Phenomenology of Court-Ordered Treatment: From the Perspective of Methamphetamine Dependent Adults

This phenomenological study was designed to explore with a sample of methamphetamine dependent adults their perceptions of the process involved in their experiences of court-ordered treatment. The motivation for this study derives from the researcher\u27s wish to unearth ways to better understand and support the needs of adults suffering from addiction. A significant amount of research has already been conducted in regards to the treatment of methamphetamine addiction from the standpoint of quantitative measurements of treatment outcomes, but limited information is presently available from the perspective of the suffers. The stringent selection of the sample was composed of six individuals with prior histories of being court-ordered to drug treatment for methamphetamine use. The participants were drawn from Narcotics and Alcohol Anonymous groups in the Snohomish and King County regions of Washington State. The collection of data was primarily through the means of structured interviews that offered space for the individuals\u27 perspectives to emerge. A brief survey was utilized as a supportive method to collect demographic information of the participants. This study gathered the statements of the participants and focused on the emergent themes that were collectively expressed among the participants\u27 experiences. This research revealed the positive and negative impressions felt towards the court system and treatment processes. The findings showed that the court system experience was an incentive to enter and remain in treatment and was considered a positive once the participants accepted the obligations of the court system. The negative perceptions of the court system were due to issues related to practical concerns and perceptions of the court system as intimidating and punitive. Positive aspects of the treatment were experienced as learning skills to make positive life changes, acquiring new perceptions, learning from others and gaining a sense of community, and having positive life experiences. Negative aspects of treatment were experienced as challenges working with others (staff, counselors, and patients), lack of useful treatment interventions, and insufficient structure. Considering the various factors affect not only the treatment of individuals suffering from addiction, the recommendations address the specific needs reported by the individuals in the present study. The electronic version of this dissertation is at OhioLink ETD Center,www.ohiolink.ed

Encoding and storage components of verbal working memory as revealed by a factorial design, an FMRI study

In this fMRI study, the contributions of frontal and posterior brain regions to verbal working memory were investigated. A two-factor design with low and high memory load (2 and 5 letters) and short and long delay (4 and 12 secs.) as factors were used. Based on reports in the literature, we expect activity in the following frontal and parietal brain regions of interest (ROIs): Brodmann areas (BA) 6, 9, 46, 44, 45, 7 and 40. The analysis of collected flvM data involved image processing and statistical analysis methods including realignment, spatial normalization, spatial smoothing, temporal filtering, intensity normalization, statistical tests, and thresholding of results. The design allowed for testing the interaction and main effects of the two factors. The interaction terms revealed involvement in the caudate and BA 6, 9, and 7. The main effects revealed activity in BA 6, 9, 32, 40, 44, cerebellum, thalamus, and caudate. The results of this study support the literature and offer more insight into previous findings

Characterization of mismatch between behavioral stimuli and FRMI data using the Kalman filter

The advance of blood oxygen level dependent function magnetic resonance imaging, (BOLD fMRI), allows researchers to non-invasively investigate the functioning human brain. The BOLD fMRI response to brief stimuli is called the hemodynamic response function (HRF), which can vary across brain regions and across subjects. Models of the HRF are used to increase sensitivity of statistical maps; however, they often don\u27t account for spatial and temporal variance. Physiological effects, such as learning, fatigue or habituation, introduce mismatch between statistical models and the data. Methods that use minimal a priori information and track time varying signals are able to show the processing of information over time and thereby elucidate such effects. The method of Kalman filtering was employed to characterize mismatches occurring between statistical models and BOLD data. The Kalman filter operates on data point by point. This contrasts regression techniques, that use blocks of data to find a single estimate. Functional MRI data was collected from ten subjects at Columbia University while they engaged in three visual experiments and four olfactory experiments. The Kalman filter was used to distinguish between the fMRI response to a 2 second and a 12 second visual stimulus. The results from this analysis showed the extracted responses from the two stimuli significantly differed. The same analysis was also used to distinguish between primary and secondary olfactory cortices. These brain regions have shown differential temporal responses to odorants. The extracted responses were not significantly different. Extracted responses from one stimulus (visual or olfactory) were used to test if this subject specific information would predict the next experimental session, better than standard a priori models of the data. The results of this analysis showed this not to be the case. The extracted response over time to the odorant stimuli were tractable with the Kalman filter, and shown to decay as predicted from the literature. This temporal change was hypothesized to decrease predictability from one session to the next, causing the null result. To alleviate this, models were tested for their predictability across hemisphere, within session. The results showed that inclusion of subject specific information improved this fit over other a priori models. The implications of this analysis are the ability to extract temporally varying fMRI responses over an experiment without knowledge of the expected response to a stimuli. Results of such analyzes offer a look into how the brain responds and processes stimuli over the course of an experiment. This contrasts method that offer summary, or average, results from an experiment

The Phenomenology of Court-Ordered Treatment: From the Perspective of Methamphetamine Dependent Adults

This phenomenological study was designed to explore with a sample of methamphetamine dependent adults their perceptions of the process involved in their experiences of court-ordered treatment. The motivation for this study derives from the researcher\u27s wish to unearth ways to better understand and support the needs of adults suffering from addiction. A significant amount of research has already been conducted in regards to the treatment of methamphetamine addiction from the standpoint of quantitative measurements of treatment outcomes, but limited information is presently available from the perspective of the suffers. The stringent selection of the sample was composed of six individuals with prior histories of being court-ordered to drug treatment for methamphetamine use. The participants were drawn from Narcotics and Alcohol Anonymous groups in the Snohomish and King County regions of Washington State. The collection of data was primarily through the means of structured interviews that offered space for the individuals\u27 perspectives to emerge. A brief survey was utilized as a supportive method to collect demographic information of the participants. This study gathered the statements of the participants and focused on the emergent themes that were collectively expressed among the participants\u27 experiences. This research revealed the positive and negative impressions felt towards the court system and treatment processes. The findings showed that the court system experience was an incentive to enter and remain in treatment and was considered a positive once the participants accepted the obligations of the court system. The negative perceptions of the court system were due to issues related to practical concerns and perceptions of the court system as intimidating and punitive. Positive aspects of the treatment were experienced as learning skills to make positive life changes, acquiring new perceptions, learning from others and gaining a sense of community, and having positive life experiences. Negative aspects of treatment were experienced as challenges working with others (staff, counselors, and patients), lack of useful treatment interventions, and insufficient structure. Considering the various factors affect not only the treatment of individuals suffering from addiction, the recommendations address the specific needs reported by the individuals in the present study. The electronic version of this dissertation is at OhioLink ETD Center,www.ohiolink.ed

Cognitive reserve in granulin-related frontotemporal dementia: from preclinical to clinical stages

OBJECTIVE Consistent with the cognitive reserve hypothesis, higher education and occupation attainments may help persons with neurodegenerative dementias to better withstand neuropathology before developing cognitive impairment. We tested here the cognitive reserve hypothesis in patients with frontotemporal dementia (FTD), with or without pathogenetic granulin mutations (GRN+ and GRN-), and in presymptomatic GRN mutation carriers (aGRN+). METHODS Education and occupation attainments were assessed and combined to define Reserve Index (RI) in 32 FTD patients, i.e. 12 GRN+ and 20 GRN-, and in 17 aGRN+. Changes in functional connectivity were estimated by resting state fMRI, focusing on the salience network (SN), executive network (EN) and bilateral frontoparietal networks (FPNs). Cognitive status was measured by FTD-modified Clinical Dementia Rating Scale. RESULTS In FTD patients higher level of premorbid cognitive reserve was associated with reduced connectivity within the SN and the EN. EN was more involved in FTD patients without GRN mutations, while SN was more affected in GRN pathology. In aGRN+, cognitive reserve was associated with reduced SN. CONCLUSIONS This study suggests that cognitive reserve modulates functional connectivity in patients with FTD, even in monogenic disease. In GRN inherited FTD, cognitive reserve mechanisms operate even in presymptomatic to clinical stages

The Role of Lifetime Exposures across Cognitive Domains in Barbados Using Data From the SABE Study

This study characterized the effects of aging on individual cognitive domains and how sex, job type, and years of education alter the age effect on older adults from Barbados. This was an analysis of the cross-sectional data collected as part of the SABE Study (Health, Well-being and Ageing) in 2006. The loss of a single point in each of the individual cognitive domains assessed using the mini-mental state exam served as dependent variables. Independent variables included age, sex, years of education, job type, and the interactions with age in a series of logistic regression analyses. The study aimed to identify which factors altered the effect of age on cognitive performance and which directly affected performance. Results demonstrated that the effect of age differed across the cognitive domains. In addition, sex, education, and job type all differentially affected cognitive performance in an additive, formative manner. The most consistent finding was that high years of education coupled with employment requiring mostly mental effort was the best combination for maintaining high levels of cognitive performance in late life. The results demonstrate that adverse age effects on cognitive performance may be minimized or delayed through modifiable lifetime exposures in the people of Barbados

BOLD Neurovascular Coupling Does Not Change Significantly with Normal Aging

Studies of cognitive function that compare the blood oxygenation level dependent (BOLD) signal across age groups often require the assumption that neurovascular coupling does not change with age. Tests of this assumption have produced mixed results regarding the strength of the coupling and its relative time course. Using deconvolution, we found that age does not have a significant effect on the time course of the hemodynamic impulse response function or on the slope of the BOLD versus stimulus duration relationship. These results suggest that in cognitive studies of healthy aging, group differences in BOLD activation are likely due to age-related changes in cognitive-neural interactions and information processing rather than to impairments in neurovascular coupling

The Indirect Effect of Age Group on Switch Costs Via Gray Matter Volume and Task-Related Brain Activity

Healthy aging simultaneously affects brain structure, brain function, and cognition. These effects are often investigated in isolation ignoring any relationships between them. It is plausible that age related declines in cognitive performance are the result of age-related structural and functional changes. This straightforward idea is tested in within a conceptual research model of cognitive aging. The current study tested whether age-related declines in task-performance were explained by age-related differences in brain structure and brain function using a task-switching paradigm in 175 participants. Sixty-three young and 112 old participants underwent MRI scanning of brain structure and brain activation. The experimental task was an executive context dual task with switch costs in response time as the behavioral measure. A serial mediation model was applied voxel-wise throughout the brain testing all pathways between age group, gray matter volume, brain activation and increased switch costs, worsening performance. There were widespread age group differences in gray matter volume and brain activation. Switch costs also significantly differed by age group. There were brain regions demonstrating significant indirect effects of age group on switch costs via the pathway through gray matter volume and brain activation. These were in the bilateral precuneus, bilateral parietal cortex, the left precentral gyrus, cerebellum, fusiform, and occipital cortices. There were also significant indirect effects via the brain activation pathway after controlling for gray matter volume. These effects were in the cerebellum, occipital cortex, left precentral gyrus, bilateral supramarginal, bilateral parietal, precuneus, middle cingulate extending to medial superior frontal gyri and the left middle frontal gyri. There were no significant effects through the gray matter volume alone pathway. These results demonstrate that a large proportion of the age group effect on switch costs can be attributed to individual differences in gray matter volume and brain activation. Therefore, age-related neural effects underlying cognitive control are a complex interaction between brain structure and function. Furthermore, the analyses demonstrate the feasibility of utilizing multiple neuroimaging modalities within a conceptual research model of cognitive aging