The Center for Integrated Molecular Brain Imaging (Cimbi) database.

We here describe a multimodality neuroimaging containing data from healthy volunteers and patients, acquired within the Lundbeck Foundation Center for Integrated Molecular Brain Imaging (Cimbi) in Copenhagen, Denmark. The data is of particular relevance for neurobiological research questions related to the serotonergic transmitter system with its normative data on the serotonergic subtype receptors 5-HT1A, 5-HT1B, 5-HT2A, and 5-HT4 and the 5-HT transporter (5-HTT), but can easily serve other purposes. The Cimbi database and Cimbi biobank were formally established in 2008 with the purpose to store the wealth of Cimbi-acquired data in a highly structured and standardized manner in accordance with the regulations issued by the Danish Data Protection Agency as well as to provide a quality-controlled resource for future hypothesis-generating and hypothesis-driven studies. The Cimbi database currently comprises a total of 1100 PET and 1000 structural and functional MRI scans and it holds a multitude of additional data, such as genetic and biochemical data, and scores from 17 self-reported questionnaires and from 11 neuropsychological paper/computer tests. The database associated Cimbi biobank currently contains blood and in some instances saliva samples from about 500 healthy volunteers and 300 patients with e.g., major depression, dementia, substance abuse, obesity, and impulsive aggression. Data continue to be added to the Cimbi database and biobank.

Lost in localization: a solution with neuroinformatics 2.0?

The commentary by Derrfuss and Mar (Derrfuss, J., Mar, R.A., 2009. Lost in localization: The need for a universal coordinate database. NeuroImage, doi:10.1016/j.neuroimage.2009.01.053.) discusses some of the limitations of the present databases and calls for a universal coordinate database. Here I discuss further issues and propose another angle to the solution of a universal coordinate database with the use of wiki technology.

Mining for associations between text and brain activation in a functional neuroimaging database.

We describe a method for mining a neuroimaging database for associations between text and brain locations. The objective is to discover association rules between words indicative of cognitive function as described in abstracts of neuroscience papers and sets of reported stereotactic Talairach coordinates. We invoke a simple probabilistic framework in which kernel density estimates are used to model distributions of brain activation foci conditioned on words in a given abstract. The principal associations are found in the joint probability density between words and voxels. We show that the statistically motivated associations are well aligned with general neuroscientific knowledge.

Finding related functional neuroimaging volumes.

We describe a content-based image retrieval technique for finding related functional neuroimaging experiments by voxelization of sets of stereotactic coordinates in Talairach space, comparing the volumes and reporting related volumes in a sorted list. Voxelization is accomplished by convolving each coordinate with a Gaussian kernel. The scheme allows us to compare experiments represented as either lists of coordinates or volumes, and we introduce alternative entrances to databases by image-based indices constructed via novelty measures and singular value decomposition.

Exploring fMRI data for periodic signal components.

We use a Bayesian framework to detect periodic components in fMRI data. The resulting detector is sensitive to periodic components with a flexible number of harmonics and with arbitrary amplitude and phases of the harmonics. It is possible to detect the correct number of harmonics in periodic signals even if the fundamental frequency is beyond the Nyquist frequency. We apply the signal detector to locate regions that are highly affected by periodic physiological artifacts, such as cardiac pulsation.

Brede tools and federating online neuroinformatics databases.

As open science neuroinformatics databases the Brede Database and Brede Wiki seek to make distribution and federation of their content as easy and transparent as possible. The databases rely on simple formats and allow other online tools to reuse their content. This paper describes the possible interconnections on different levels between the Brede tools and other databases.

Action and language mechanisms in the brain: data, models and neuroinformatics.

We assess the challenges of studying action and language mechanisms in the brain, both singly and in relation to each other to provide a novel perspective on neuroinformatics, integrating the development of databases for encoding ­ separately or together ­ neurocomputational models and empirical data that serve systems and cognitive neuroscience.

Endogenous plasma estradiol in healthy men is positively correlated with cerebral cortical serotonin 2A receptor binding.

BACKGROUND: Sex-hormones influence brain function and are likely to play a role in the gender predisposition to mood and anxiety disorders. Acute fluctuations of sex-hormone levels including hormonal replacement therapy appear to affect serotonergic neurotransmission, but it is unknown if baseline levels affect serotonergic neurotransmission. This study was undertaken to examine if baseline levels of endogenous sex hormones are associated with cerebral serotonin 2A (5-HT(2A)) receptor binding in men. METHODS: In a group of 72 healthy men (mean age 37.5 years ±17.4 SD, range 19.6-81.7) we studied the effect of plasma sex hormone levels on neocortical 5-HT(2A) receptor binding as imaged with [(18)F]altanserin PET. The effect of endogenous sex-hormone levels was evaluated by multiple linear regression analysis. RESULTS: Mean neocortical 5-HT(2A) receptor binding was positively correlated with estradiol (p=0.0001), whereas no independent effects of testosterone could be demonstrated. Correction for other factors of importance for 5-HT(2A) receptor binding did not change the result. A voxel-based analysis suggested that there were no regional differences in the estradiol effect on cortical 5-HT(2A) receptor binding. CONCLUSIONS: Our data show a positive correlation between endogenous plasma estradiol levels and cortical 5-HT(2A) receptor binding in healthy men, whereas, no independent effect of testosterone was demonstrated. We speculate that this association could be mediated through effects on gene transcription.

Visualizing data mining results with the brede tools.

A few neuroinformatics databases now exist that record results from neuroimaging studies in the form of brain coordinates in stereotaxic space. The Brede Toolbox was originally developed to extract, analyze and visualize data from one of them - the BrainMap database. Since then the Brede Toolbox has expanded and now includes its own database with coordinates along with ontologies for brain regions and functions: The Brede Database. With Brede Toolbox and Database combined, we setup automated workflows for extraction of data, mass meta-analytic data mining and visualizations. Most of the Web presence of the Brede Database is established by a single script executing a workflow involving these steps together with a final generation of Web pages with embedded visualizations and links to interactive three-dimensional models in the Virtual Reality Modeling Language. Apart from the Brede tools I briefly review alternate visualization tools and methods for Internet-based visualization and information visualization as well as portals for visualization tools.

Mining the posterior cingulate: segregation between memory and pain components.

We present a general method for automatic meta-analyses in neuroscience and apply it on text data from published functional imaging studies to extract main functions associated with a brain area-the posterior cingulate cortex (PCC). Abstracts from PubMed are downloaded, words extracted and converted to a bag-of-words matrix representation. The combined data are analyzed with hierarchical non-negative matrix factorization. We find that the prominent themes in the PCC corpus are episodic memory retrieval and pain. We further characterize the distribution in PCC of the Talairach coordinates available in some of the articles. This shows a tendency to functional segregation between memory and pain components where memory activations are predominantly in the caudal part and pain in the rostral part of PCC.

Modeling of activation data in the BrainMap database: detection of outliers.

We describe a system for meta-analytical modeling of activation foci from functional neuroimaging studies. Our main vehicle is a set of density models in Talairach space capturing the distribution of activation foci in sets of experiments labeled by lobar anatomy. One important use of such density models is identification of novelty, i.e., low probability database events. We rank the novelty of the outliers and investigate the cause for 21 of the most novel, finding several outliers that are entry and transcription errors or infrequent or non-conforming terminology. We briefly discuss the use of atlases for outlier detection.