Histopathology is insufficient to predict disease progression and clinical outcome in lung adenocarcinoma. Here we show that gene-expression profiles based on microarray analysis can be used to predict patient survival in early-stage lung adenocarcinomas. Genes most related to survival were identified with univariate Cox analysis. Using either two equivalent but independent training and testing sets, or 'leave-one-out' cross-validation analysis with all tumors, a risk index based on the top 50 genes identified low-risk and high-risk stage I lung adenocarcinomas, which differed significantly with respect to survival. This risk index was then validated using an independent sample of lung adenocarcinomas that predicted high- and low-risk groups. This index included genes not previously associated with survival. The identification of a set of genes that predict survival in early-stage lung adenocarcinoma allows delineation of a high-risk group that may benefit from adjuvant therapy.

Functional neuroimaging data embodies a massive multiple testing problem, where 100 000 correlated test statistics must be assessed. The familywise error rate, the chance of any false positives is the standard measure of Type I errors in multiple testing. In this paper we review and evaluate three approaches to thresholding images of test statistics: Bonferroni, random eld and the permutation test. Owing to recent developments, improved Bonferroni procedures, such as Hochberg's methods, are now applicable to dependent data. Continuous random eld methods use the smoothness of the image to adapt to the severity of the multiple testing problem. Also, increased computing power has made both permutation and bootstrap methods applicable to functional neuroimaging. We evaluate these approaches on t images using simulations and a collection of real datasets. We nd that Bonferroni-related tests offer little improvement over Bonferroni, while the permutation method offers substantial improvement over the random eld method for low smoothness and low degrees of freedom. We also show the limitations of trying to nd an equivalent number of independent tests for an image of correlated test statistics.

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Small-world networks, according to Watts and Strogatz, are a class of networks that are ''highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.'' These characteristics result in networks with unique properties of regional specialization with efficient information transfer. Social networks are intuitive examples of this organization, in which cliques or clusters of friends being interconnected but each person is really only five or six people away from anyone else. Although this qualitative definition has prevailed in network science theory, in application, the standard quantitative application is to compare path length (a surrogate measure of distributed processing) and clustering (a surrogate measure of regional specialization) to an equivalent random network. It is demonstrated here that comparing network clustering to that of a random network can result in aberrant findings and that networks once thought to exhibit small-world properties may not. We propose a new small-world metric, x (omega), which compares network clustering to an equivalent lattice network and path length to a random network, as Watts and Strogatz originally described. Example networks are presented that would be interpreted as small-world when clustering is compared to a random network but are not small-world according to x. These findings have important implications in network science because small-world networks have unique topological properties, and it is critical to accurately distinguish them from networks without simultaneous high clustering and short path length.

Small-world networks are a class of networks that exhibit efficient long-distance communication and tightly interconnected local neighborhoods. In recent years, functional and structural brain networks have been examined using network theory-based methods, and consistently shown to have small-world properties. Moreover, some voxel-based brain networks exhibited properties of scale-free networks, a class of networks with mega-hubs. However, there are considerable inconsistencies across studies in the methods used and the results observed, particularly between region-based and voxel-based brain networks. We constructed functional brain networks at multiple resolutions using the same resting-state fMRI data, and compared various network metrics, degree distribution, and localization of nodes of interest. It was found that the networks with higher resolutions exhibited the properties of small-world networks more prominently. It was also found that voxel-based networks were more robust against network fragmentation compared to region-based networks. Although the degree distributions of all networks followed an exponentially truncated power law rather than true power law, the higher the resolution, the closer the distribution was to a power law. The voxel-based analyses also enhanced visualization of the results in the 3D brain space. It was found that nodes with high connectivity tended have high efficiency, a co-localization of properties that was not as consistently observed in the region-based networks. Our results demonstrate benefits of constructing the brain network at the finest scale the experiment will permit.

No abstract

In recent years multiple brain MR imaging modalities have emerged; however, analysis methodologies have mainly remained modality specific. In addition, when comparing across imaging modalities, most researchers have been forced to rely on simple region-of-interest type analyses, which do not allow the voxel-by-voxel comparisons necessary to answer more sophisticated neuroscience questions. To overcome these limitations, we developed a toolbox for multimodal image analysis called biological parametric mapping (BPM), based on a voxel-wise use of the general linear model. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in MATLAB with a user friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely-used T-field, has been implemented in the correlation analysis for more accurate results. An example with in-vivo data is presented demonstrating the potential of the BPM methodology as a tool for multimodal image analysis.

Recent developments in network theory have allowed for the study of the structure and function of the human brain in terms of a network of interconnected components. Among the many nodes that form a network, some play a crucial role and are said to be central within the network structure. Central nodes may be identified via centrality metrics, with degree, betweenness, and eigenvector centrality being three of the most popular measures. Degree identifies the most connected nodes, whereas betweenness centrality identifies those located on the most traveled paths. Eigenvector centrality considers nodes connected to other high degree nodes as highly central. In the work presented here, we propose a new centrality metric called leverage centrality that considers the extent of connectivity of a node relative to the connectivity of its neighbors. The leverage centrality of a node in a network is determined by the extent to which its immediate neighbors rely on that node for information. Although similar in concept, there are essential differences between eigenvector and leverage centrality that are discussed in this manuscript. Degree, betweenness, eigenvector, and leverage centrality were compared using functional brain networks generated from healthy volunteers. Functional cartography was also used to identify neighborhood hubs (nodes with high degree within a network neighborhood). Provincial hubs provide structure within the local community, and connector hubs mediate connections between multiple communities. Leverage proved to yield information that was not captured by degree, betweenness, or eigenvector centrality and was more accurate at identifying neighborhood hubs. We propose that this metric may be able to identify critical nodes that are highly influential within the network.