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In parallel with standard model-based methods for the analysis of fMRI data, exploratory methods--such as PCA, ICA, and clustering--have been developed to give an account of the dataset with minimal priors: no assumption is made on the data content itself, but the data structure is assumed to show some properties (decorrelation, independence) that allow for the detection of structures of interest. In this paper, we present an alternative that tries to take into account some relevant knowledge for the analysis of the dataset, e.g., the experimental paradigm, while keeping the flexibility of exploratory methods: we use a prior temporal modeling of the data that characterizes each voxel time course. Two implementations are proposed: one based on the General Linear Model, the other one on more flexible short-term predictors, whose complexity is controlled by a Minimum Description Length approach. However, our main concern here is the construction of a multivariate model; the latter is performed with the help of a kernel PCA method that builds a redundant representation of the data through the nonlinearity of the kernel. This allows for a refinement in the description of the (temporal) patterns of interest. In particular, this helps in the characterization of subtle variations in the response to different experimental conditions. We illustrate the usefulness of nonlinearity through the analysis of a synthetic dataset and show on a real dataset how it helps to interpret the experimental results.
Neuroimage 2003 Sep
PMID:Dynamical components analysis of fMRI data through kernel PCA. 1452 68

Falkenstein, Hohnsbein, and Hoorman (1994) suggested that common measures of P300 latency confound a "P-SR" component whose latency corresponds to stimulus evaluation time and a "P-CR" component whose latency varies with response-selection time, thus casting doubt on work in mental chronometry that relies on P300 latency. We report here a replication and extension of Falkenstein et al. (1994) using a high-density 129-electrode montage with 11 subjects. Spatiotemporal PCA was used to extract the components of the ERP. A centroid measure is also introduced for detecting waveform-timing changes beyond just peak latency. In terms of componentry, we argue that the P-SR and the P-CR, correspond to the P3a/Novelty P3 and the P300, respectively. Conceptually, we dispute the proposed distinction between stimulus evaluation and response selection. We suggest a four-stage ERP model of information processing and place the P3a and the P300 in this framework.
Psychophysiology 2004 Sep
PMID:Parsing the late positive complex: mental chronometry and the ERP components that inhabit the neighborhood of the P300. 1531 73

The dual serotonin (5-HT) re-uptake inhibitor and 5-HT(1A) receptor agonist vilazodone was found to increase central serotonin levels in rat brain. In the course of structural modifications of vilazodone 3-[4-[4-(2-oxo-2H-1-benzopyran-6-yl)-1-piperazinyl]-butyl]-1H-indole-5-carbonitrile 8i and its fluorine analogue 6-[4-[4-(5-fluor-3-indolyl)-butyl]-1-piperazinyl]-2H-1-benzopyran-2-one have been identified. These unsubstituted chromenones are equally potent at the 5-HT(1A) receptor and 5-HT transporter. The implementation of nitrogen functionalities in position 3 of the chromenones resulted in compounds acting as agonists at the 5-HT(1A) receptor and as 5-HT re-uptake inhibitors like vilazodone. Ex vivo 5-HT re-uptake inhibition and in vitro 5-HT agonism were determined in the PCA- and GTPgammaS-assay, respectively. The potential of these chromenones to increase central 5-HT levels was measured in microdialysis studies and especially the derivatives 3-[4-[4-(3-amino-2-oxo-2H-chromen-6-yl)-piperazin-1-yl]-butyl]-1H-indole-5-carbonitrile 8f, ethyl (6-[4-[4-(5-cyano-1H-indol-3-yl)-butyl]-piperazin-1-yl]-2-oxo-2H-chromen-3-yl)-carbamate 8h and N-(6-[4-[4-(5-cyano-1H-indol-3-yl)-butyl]-piperazin-1-yl]-2-oxo-2H-chromen-3-yl)-acetamide 8k give rise to rapid development of increased serotonin levels in rat brain cortex, lasting longer than 3h.
Bioorg Med Chem 2004 Sep 15
PMID:Dual 5-HT1A agonists and 5-HT re-uptake inhibitors by combination of indole-butyl-amine and chromenonyl-piperazine structural elements in a single molecular entity. 1533 63

We previously showed that specific strains of human immunodeficiency virus (HIV)-1 infect the brain and contribute to Neuropathology, Cognitive Distress, and Neuropsychiatric Disease. To study further brain disease that results from HIV-1 infection, we commenced analysis of changes in gene expression in brain. We analyzed RNA purified from Frontal Cortex of 5 HIV-1 infected and 4 HIV-1 negative control subjects RNA was amplified and Affymetrix technology was used to analyze gene expression using the 12,585 gene Affymetrix Human Genome U95A chip. The expressed genes showed highly significant Pearsons correlations with each other within the two groups. Expression intensities were transferred to Microsoft Excel and Spotfire was used to analyze the results. Twenty-group K-means cluster analysis was done for HIV+ and HIV- subjects. Genes that were expressed in the same cluster numbers in the two groups were removed from further analysis. Analysis of Gene expression in the top 13 HIV+ clusters showed expression in the 40 gene categories designated in our prior studies. Genes from several categories occurred in more than one K-means cluster. Genes identified in these lists included several genes that have been previously studied: MBP, Myelin-PLP, NMDA receptor, MAG, astrocytic protein, Notch 3, APP, Senescence, proteasome, Ferritin, signaling, cell cycle, iNOS, Chemokine, splicing, synapse, protein tags, and ribosomal proteins. The first (primary significant) axis of both Principal Component Analyses ordered the genes in the same patient groups as the K-means cluster analysis for the respective patient groups. PCA was thus not more informative than K-Means cluster analysis. Ratios of HIV+ to HIV- intensities were calculated for all the averaged gene expression intensities. The ratio range was 0.14 to 9.26. The genes at the extremes (ad extrema) did not correspond to the gene order by K-means clustering (or PCA). The genes in the top 13 K-means clusters showed low-level changes by expression ratio. Genes ad extrema by ratio were in clusters with very large memberships. Mann-Whitney analysis confirmed expression ratio results. Several inferences result from our preliminary study. First, study design will be different in future studies involving additional replicates. Second, ratios inform us of the extent of changes in gene expression quantitatively. Third, Cluster methodology provides us with more subtle information, how bunches (clusters) of genes behave in terms of their centroids (attractors). Fourth, genes that change extensively by ratio tend to be in the larger k-Means clusters. We conclude that ranking gene expression with the use of expression ratio or by K-means clustering, yield different representations of the data.
Front Biosci 2004 Sep 01
PMID:Analytic approaches to differential gene expression in AIDS versus control brains. 1535 27

We describe a new 3-D statistical shape model of the heart consisting of atria, ventricles and epicardium. The model was constructed by combining information on standard short- and long-axis cardiac MR images. In the model, the variability of the shape was modeled with PCA- and ICA-based shape models as well as with non-parametric landmark probability distributions and a probabilistic atlas. The statistical atlas was built from 25 healthy subjects. The shape model was evaluated by applying it to image segmentation. The probabilistic atlas was found to be superior to the other shape models (P < 0.001) in this study.
Med Image Anal 2004 Sep
PMID:Statistical shape model of atria, ventricles and epicardium from short- and long-axis MR images. 1545 Feb 30

PCA, LDA, and Bayesian analysis are the three most representative subspace face recognition approaches. In this paper, we show that they can be unified under the same framework. We first model face difference with three components: intrinsic difference, transformation difference, and noise. A unified framework is then constructed by using this face difference model and a detailed subspace analysis on the three components. We explain the inherent relationship among different subspace methods and their unique contributions to the extraction of discriminating information from the face difference. Based on the framework, a unified subspace analysis method is developed using PCA, Bayes, and LDA as three steps. A 3D parameter space is constructed using the three subspace dimensions as axes. Searching through this parameter space, we achieve better recognition performance than standard subspace methods.
IEEE Trans Pattern Anal Mach Intell 2004 Sep
PMID:A unified framework for subspace face recognition. 1574 96

Connectionist networks have been criticized for their inability to represent complex structures with systematicity. That is, while they can be trained to represent and manipulate complex objects made of several constituents, they generally fail to generalize to novel combinations of the same constituents. This paper presents a modification of Pollack's Recursive Auto-Associative Memory (RAAM), that addresses this criticism. The network uses linear units and is trained with Oja's rule, in which it generalizes PCA to tree-structured data. Learned representations may be linearly combined, in order to represent new complex structures. This results in unprecedented generalization capabilities. Capacity is orders of magnitude higher than that of a RAAM trained with back-propagation. Moreover, regularities of the training set are preserved in the new formed objects. The formation of new structures displays developmental effects similar to those observed in children when learning to generalize about the argument structure of verbs.
Neural Netw 2005 Sep
PMID:Linear recursive distributed representations. 1593 73

The prevalidation strategy was applied to evaluate UV-vis spectrophotometric procedure with Folin-Ciocalteu's reagent for polyphenols determination. Favourable prevalidation characteristics verified this procedure as a valuable tool in polyphenols analysis and it was successfully applied for determination of total polyphenols and tannins in leaves, stems and flowers of Plantago L. species growing in Croatia. The results showed the variety of total polyphenols content between different plant parts (leaves: up to 10.15%; stems: up to 4.34% and flowers: up to 5.56%). The content of tannins in stems was from 0.28% to 1.00%, while leaves and flowers contained tannins in concentrations of 2.26% and 2.21%, respectively. The results of polyphenols determination were evaluated by using multivariate analysis (UPGMA and PCA) as a contribution to elucidation of relations between different taxa of genus Plantago L.
J Pharm Biomed Anal 2005 Sep 15
PMID:Spectrophotometric method for polyphenols analysis: prevalidation and application on Plantago L. species. 1597 69

Decrease in self-esteem (SE) is found in all mood disorders during inter-episode phases. This trait was associated with relapse and suicidality but its genetic basis is still undefined, probably because SE has multiple components. The aim of the current study was to ascertain which of those components were altered in a sample of affective patients. Three hundred and thirty-one outpatients with bipolar (N=199) and major depressive MD (N=132) disorders in remission for at least three months and one hundred controls completed the Rosenberg Self-esteem Scale (RSE; [Rosenberg, M., 1965. The measurement of self-esteem, Society and the Adolescent Self-Image. Princeton University Press, pp.16-36]). Principal component analysis was performed to identify RSE factor structure. Extracted factors were compared across case and control groups in the whole sample (N=431) and in a sub-sample (N=301) with low self-esteem (RSE <20). PCA yielded a two-factor solution with self-confidence (SC) and self-deprecation (SD) that was largely consistent with the existing literature. Such factors were both associated with lower scores in affective patients than controls (SC: F=52, p<0.01; SD: F=43, p<0.01). However in the low RSE group only self-confidence was found to be decreased in subjects with mood disorders (SC: F=13.8, p<0.01; SD: F=0.05, p=0.9). These findings suggest that self-esteem deficit in affective disorders might involve specific components. Implications for research and clinical practice are discussed.
J Affect Disord 2005 Sep
PMID:Components of self-esteem in affective patients and non-psychiatric controls. 1604 Jan 27

We investigated whether blocking afferent nociceptive inputs by continuous intra- and postoperative thoracic epidural analgesia (TEA) would decrease plasma concentrations of brain natriuretic peptide (BNP) in patients who were at risk for, or had, coronary artery disease. Twenty-eight patients undergoing major abdominal surgery received either general anesthesia supplemented with a continuous thoracic epidural infusion of 1.25 mg/mL bupivacaine and 1 microg/mL sufentanil (n = 14; TEA) or general anesthesia followed by IV patient-controlled analgesia (n = 14; IV PCA). Visual analog scale pain scores, hemodynamics, plasma catecholamines, cardiac troponin T, atrial natriuretic peptide (ANP), and BNP were serially measured preoperatively, 90 min after skin incision, at arrival in the intensive care unit, and in the morning of the first, second, and third postoperative day. Dynamic visual analog scale scores were significantly less in the TEA group. TEA reduced the postoperative heart rate without affecting other hemodynamic variables. Plasma epinephrine increased perioperatively in both groups but was significantly lower in the TEA group. Baseline ANP and BNP concentrations were similar between groups (TEA 3.4 +/- 1.8 and 27.0 +/- 12.3 pg/mL; IV PCA 3.1 +/- 2.0 and 25.9 +/- 13.0 pg/mL, respectively). ANP and BNP increased perioperatively in both groups, with significantly lower postoperative BNP levels in TEA patients (TEA 92.1 +/- 31.9 pg/mL; IV PCA 161.2 +/- 44.7 pg/mL). No such difference was observed in plasma ANP concentrations. Plasma cardiac troponin T concentrations were within normal limits in both groups at all times. We conclude that continuous perioperative TEA using local anesthetics and opioids attenuated the release of BNP in patients undergoing major abdominal surgery who were at risk for, or had, coronary artery disease.
Anesth Analg 2005 Sep
PMID:Continuous intra- and postoperative thoracic epidural analgesia attenuates brain natriuretic peptide release after major abdominal surgery. 2145 Oct 68


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