SETA: a novel SH3 domain-containing adapter molecule associated with malignancy in astrocytes. (73/561)

Differential display polymerase chain reaction analysis was used to compare five differentiation states of the O-2A progenitor-like cell line CG4: progenitor cells and cells at 12 h or 4 days after the induction of differentiation into oligodendrocytes or astrocytes. This led to the identification of 52 sequence tags that were expressed differentially with cellular phenotype. One sequence was upregulated during differentiation of CG4 cells and represented a novel gene that we named SETA (SH3 domain-containing gene expressed in tumorigenic astrocytes). This gene encodes an SH3 domain-containing adapter protein with sequence similarity to the CD2AP (CD2 adapter protein) and CMS (Cas ligand with multiple Src homology) genes. SETA mRNA was expressed at high levels in the developing rat brain but was barely detectable in the normal adult rat or human brain. However, SETA mRNA was found in approximately one half of the human gliomas tested, including astrocytomas grades II, III, and IV, as well as oligodendrogliomas, mixed oligoastrocytomas, and human glioma-derived cell lines. A rat glioma generated by treatment with the alkylating carcinogen ethylnitrosourea on postnatal day 1 and a derived cell line also expressed SETA mRNA. Furthermore, in an in vitro model of astrocytoma progression based on p53-/- astrocytes, expression of SETA was restricted to cells that are tumorigenic.  (+info)

Spatial structure of cone inputs to color cells in alert macaque primary visual cortex (V-1). (74/561)

The spatial structure of color cell receptive fields is controversial. Here, spots of light that selectively modulate one class of cones (L, M, or S, or loosely red, green, or blue) were flashed in and around the receptive fields of V-1 color cells to map the spatial structure of the cone inputs. The maps generated using these cone-isolating stimuli and an eye-position-corrected reverse correlation technique produced four findings. First, the receptive fields were Double-Opponent, an organization of spatial and chromatic opponency critical for color constancy and color contrast. Optimally stimulating both center and surround subregions with adjacent red and green spots excited the cells more than stimulating a single subregion. Second, red-green cells responded in a luminance-invariant way. For example, red-on-center cells were excited equally by a stimulus that increased L-cone activity (appearing bright red) and by a stimulus that decreased M-cone activity (appearing dark red). This implies that the opponency between L and M is balanced and argues that these cells are encoding a single chromatic axis. Third, most color cells responded to stimuli of all orientations and had circularly symmetric receptive fields. Some cells, however, showed a coarse orientation preference. This was reflected in the receptive fields as oriented Double-Opponent subregions. Fourth, red-green cells often responded to S-cone stimuli. Responses to M- and S-cone stimuli usually aligned, suggesting that these cells might be red-cyan. In summary, red-green (or red-cyan) cells, along with blue-yellow and black-white cells, establish three chromatic axes that are sufficient to describe all of color space.  (+info)

Pictorial outcome measures for the hospital care of older patients--a suggested toolkit. (75/561)

OBJECTIVE: to propose three pictorial methods of presenting hospital outcome data, suitable for use in older patients entering medical specialties (including rehabilitation). PATIENTS: 224 patients (mean age 80.6 years, 56% female, 75% emergencies) admitted to a department of medicine for the elderly. PRESENTATIONAL TECHNIQUES: the methods we propose for the presentation of outcome data are (i) place of discharge, using a two-dimensional diagram; (ii) 'survival' analyses, but using discharge from hospital rather than death as the endpoint; and (iii) 'phase diagrams', a novel method of charting the progress of a cohort of patients. To illustrate these methods, the relationship between admission case-mix (with patients put into tertiles on the basis of their Barthel index score) and outcome is shown graphically. RESULT: each of the three techniques has different relative strengths, but their pictorial nature allows for rapid interpretation of data, showing, for example, the marked influence of case-mix. Separate analyses of subgroups of patients (such as those who die in hospital and those who survive) are also readily attainable by the three methods. CONCLUSIONS: the three methods of presenting outcome should be of benefit in comparing the performance of different units, particularly when case-mix is taken into account. The pictorial methods are complementary both to more conventional patient-based methods (mean duration of stay, median duration of stay, percentile duration of stay, regression analyses etc) and to modelling techniques using 'census' data from large numbers of patients.  (+info)

Impaired spatial working memory across saccades contributes to abnormal search in parietal neglect. (76/561)

Visual neglect of left space following right parietal damage in humans involves a lateral bias in attention, apparent in many search tasks. We hypothesized that parietal neglect may also involve a failure to remember which locations have already been examined during visual search: an impairment in retaining searched locations across saccades. Using a new paradigm, we monitored gaze during search, while simultaneously probing whether observers judged they had found a new target, or judged instead that they were re-fixating a previously examined target. A patient with left neglect following focal right parietal infarction repeatedly re-fixated right locations. Critically, he often failed to remember that these locations had already been searched, treating old targets as new discoveries at an abnormal rate. In comparison, healthy age-matched control subjects rarely re-fixated targets, and mistook old targets as new targets even more rarely. The frequency of such mistakes in the parietal patient, for different conditions, correlated with the severity of his neglect. Control experiments indicated no perceptual localization deficit in non-search tasks. These results suggest a deficit in retaining searched locations across saccades in parietal neglect, in addition to the lateral spatial bias. Moreover, the former deficit exacerbates the latter, such that patients do not realize that the rightward locations favoured by their bias have already been examined during previous fixations and, for this reason, they saccade back to them repeatedly. The combination of the two deficits (a lateral bias plus a deficit in retaining locations already searched) may thus explain the pathological pattern of search that characterizes parietal neglect: why stimuli on the right are re-examined recursively, as if being searched for the first time, and hence why stimuli on the left continue to be ignored even with unlimited viewing time. These proposals accord with recent electrophysiological and functional imaging data, demonstrating posterior parietal involvement in the retention of target locations across saccades.  (+info)

Fast detection and characterization of vessels in very large 3-D data sets using geometrical moments. (77/561)

An improved and very fast algorithm dealing with the extraction of vessels in three-dimensional imaging is described. The approach is based on geometrical moments and a local cylindrical approximation. A robust estimation of vessel and background intensity levels, position, orientation, and diameter of the vessels with adaptive control of key parameters, is provided during vessel tracking. Experimental results are presented for lower limb arteries in multidetector computed tomography scanner.  (+info)

Uniform integration of genome mapping data using intersection graphs. (78/561)

MOTIVATION: The methods for analyzing overlap data are distinct from those for analyzing probe data, making integration of the two forms awkward. Conversion of overlap data to probe-like data elements would facilitate comparison and uniform integration of overlap data and probe data using software developed for analysis of STS data. RESULTS: We show that overlap data can be effectively converted to probe-like data elements by extracting maximal sets of mutually overlapping clones. We call these sets virtual probes, since each set determines a site in the genome corresponding to the region which is common among the clones of the set. Finding the virtual probes is equivalent to finding the maximal cliques of a graph. We modify a known maximal-clique algorithm such that it finds all virtual probes in a large dataset within minutes. We illustrate the algorithm by converting fingerprint and Alu-PCR overlap data to virtual probes. The virtual probes are then analyzed using double-linkage intersection graphs and structure graphs to show that methods designed for STS data are also applicable to overlap data represented as virtual probes. Next we show that virtual probes can produce a uniform integration of different kinds of mapping data, in particular STS probe data and fingerprint and Alu-PCR overlap data. The integrated virtual probes produce longer double-linkage contigs than STS probes alone, and in conjunction with structure graphs they facilitate the identification and elimination of anomalies. Thus, the virtual-probe technique provides: (i) a new way to examine overlap data; (ii) a basis on which to compare overlap data and probe data using the same systems and standards; and (iii) a unique and useful way to uniformly integrate overlap data with probe data.  (+info)

Missing value estimation methods for DNA microarrays. (79/561)

MOTIVATION: Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array values as input. For example, methods such as hierarchical clustering and K-means clustering are not robust to missing data, and may lose effectiveness even with a few missing values. Methods for imputing missing data are needed, therefore, to minimize the effect of incomplete data sets on analyses, and to increase the range of data sets to which these algorithms can be applied. In this report, we investigate automated methods for estimating missing data. RESULTS: We present a comparative study of several methods for the estimation of missing values in gene microarray data. We implemented and evaluated three methods: a Singular Value Decomposition (SVD) based method (SVDimpute), weighted K-nearest neighbors (KNNimpute), and row average. We evaluated the methods using a variety of parameter settings and over different real data sets, and assessed the robustness of the imputation methods to the amount of missing data over the range of 1--20% missing values. We show that KNNimpute appears to provide a more robust and sensitive method for missing value estimation than SVDimpute, and both SVDimpute and KNNimpute surpass the commonly used row average method (as well as filling missing values with zeros). We report results of the comparative experiments and provide recommendations and tools for accurate estimation of missing microarray data under a variety of conditions.  (+info)

MAPS: a microarray project system for gene expression experiment information and data validation. (80/561)

SUMMARY: MAPS is a MicroArray Project System for management and interpretation of microarray gene expression experiment information and data. Microarray project information is organized to track experiments and results that are: (1) validated by performing analysis on stored replicate gene expression data; and (2) queried according to the biological classifications of genes deposited on microarray chips.  (+info)