Hierarchical Shape Description of Objects by Selection and Modification of Prototypes

An approach towards shape description, based on prototype modification and generalized cylinders, has been developed and applied to the object domains pottery and polyhedra: (1) A program describes and identifies pottery from vase outlines entered as lists of points. The descriptions have been modeled after descriptions by archeologists, with the result that identifications made by the program are remarkably consisten with those of the archeologists. It has been possible to quantify their shape descriptors, which are everyday terms in our language applied to many sorts of objects besides pottery, so that the resulting descriptions seem very natural. (2) New parsing strategies for polyhedra overcome some limitations of previous work. A special feature is that the processes of parsing and identification are carried out simultaneously.

Identification, Selection, and Enrichment of Cardiomyocyte Precursors

The large-scale production of cardiomyocytes is a key step in the development of cell therapy and tissue engineering to treat cardiovascular diseases, particularly those caused by ischemia. the main objective of this study was to establish a procedure for the efficient production of cardiomyocytes by reprogramming mesenchymal stem cells from adipose tissue. First, lentiviral vectors expressing neoR and GFP under the control of promoters expressed specifically during cardiomyogenesis were constructed to monitor cell reprogramming into precardiomyocytes and to select cells for amplification and characterization. Cellular reprogramming was performed using 5'-azacytidine followed by electroporation with plasmid pOKS2a, which expressed Oct4, Sox2, and Klf4. Under these conditions, GFP expression began only after transfection with pOKS2a, and less than 0.015% of cells were GFP(+). These GFP(+) cells were selected for G418 resistance to find molecular markers of cardiomyocytes by RT-PCR and immunocytochemistry. Both genetic and protein markers of cardiomyocytes were present in the selected cells, with some variations among them. Cell doubling time did not change after selection. Together, these results indicate that enrichment with vectors expressing GFP and neoR under cardiomyocyte-specific promoters can produce large numbers of cardiomyocyte precursors (CMPs), which can then be differentiated terminally for cell therapy and tissue engineering.

Rough set feature selection and rule induction for prediction of malignancy degree in brain glioma

X. Wang, J. Yang, R. Jensen and X. Liu, 'Rough Set Feature Selection and Rule Induction for Prediction of Malignancy Degree in Brain Glioma,' Computer Methods and Programs in Biomedicine, vol. 83, no. 2, pp. 147-156, 2006.

Approximation-based feature selection and application for algae population estimation

Q. Shen and R. Jensen, 'Approximation-based feature selection and application for algae population estimation,' Applied Intelligence, vol. 28, no. 2, pp. 167-181, 2008. Sponsorship: EPSRC RONO: EP/E058388/1

Contour Generator Points for Threshold Selection and a Novel Photo-Consistency Measure for Space Carving

Space carving has emerged as a powerful method for multiview scene reconstruction. Although a wide variety of methods have been proposed, the quality of the reconstruction remains highly-dependent on the photometric consistency measure, and the threshold used to carve away voxels. In this paper, we present a novel photo-consistency measure that is motivated by a multiset variant of the chamfer distance. The new measure is robust to high amounts of within-view color variance and also takes into account the projection angles of back-projected pixels. Another critical issue in space carving is the selection of the photo-consistency threshold used to determine what surface voxels are kept or carved away. In this paper, a reliable threshold selection technique is proposed that examines the photo-consistency values at contour generator points. Contour generators are points that lie on both the surface of the object and the visual hull. To determine the threshold, a percentile ranking of the photo-consistency values of these generator points is used. This improved technique is applicable to a wide variety of photo-consistency measures, including the new measure presented in this paper. Also presented in this paper is a method to choose between photo-consistency measures, and voxel array resolutions prior to carving using receiver operating characteristic (ROC) curves.

Neural Dynamics of Saccadic and Smooth Pursuit Eye Movement Coordination during Visual Tracking of Unpredictably Moving Targets

How does the brain use eye movements to track objects that move in unpredictable directions and speeds? Saccadic eye movements rapidly foveate peripheral visual or auditory targets and smooth pursuit eye movements keep the fovea pointed toward an attended moving target. Analyses of tracking data in monkeys and humans reveal systematic deviations from predictions of the simplest model of saccade-pursuit interactions, which would use no interactions other than common target selection and recruitment of shared motoneurons. Instead, saccadic and smooth pursuit movements cooperate to cancel errors of gaze position and velocity, and thus to maximize target visibility through time. How are these two systems coordinated to promote visual localization and identification of moving targets? How are saccades calibrated to correctly foveate a target despite its continued motion during the saccade? A neural model proposes answers to such questions. The modeled interactions encompass motion processing areas MT, MST, FPA, DLPN and NRTP; saccade planning and execution areas FEF and SC; the saccadic generator in the brain stem; and the cerebellum. Simulations illustrate the model’s ability to functionally explain and quantitatively simulate anatomical, neurophysiological and behavioral data about SAC-SPEM tracking.

Sexual selection and canine dimorphism in New World monkeys.

Social and ecological factors are important in shaping sexual dimorphism in Anthropoidea, but there is also a tendency for body-size dimorphism and canine dimorphism to increase with increased body size (Rensch's rule) (Rensch: Evolution Above the Species Level. London: Methuen, 1959.) Most ecologist interpret Rensch's rule to be a consequence of social and ecological selective factors that covary with body size, but recent claims have been advanced that dimorphism is principally a consequence of selection for increased body size alone. Here we assess the effects of body size, body-size dimorphism, and social structure on canine dimorphism among platyrrhine monkeys. Platyrrhine species examined are classified into four behavioral groups reflecting the intensity of intermale competition for access to females or to limiting resources. As canine dimorphism increases, so does the level of intermale competition. Those species with monogamous and polyandrous social structures have the lowest canine dimorphism, while those with dominance rank hierarchies of males have the most canine dimorphism. Species with fission-fusion social structures and transitory intermale breeding-season competition fall between these extremes. Among platyrrhines there is a significant positive correlation between body size and canine dimorphism However, within levels of competition, no significant correlation was found between the two. Also, with increased body size, body-size dimorphism tends to increase, and this correlation holds in some cases within competition levels. In an analysis of covariance, once the level of intermale competition is controlled for, neither molar size nor molar-size dimorphism accounts for a significant part of the variance in canine dimorphism. A similar analysis using body weight as a measure of size and dimorphism yields a less clear-cut picture: body weight contributes significantly to the model when the effects of the other factors are controlled. Finally, in a model using head and body length as a measure of size and dimorphism, all factors and the interactions between them are significant. We conclude that intermale competition among platyrrhine species is the most important factor explaining variations in canine dimorphism. The significant effects of size and size dimorphism in some models may be evidence that natural (as opposed to sexual) selection also plays a role in the evolution of increased canine dimorphism.

Human CD19 and CD40L deficiencies impair antibody selection and differentially affect somatic hypermutation.

Individuals with genetic defects in CD40 ligand (CD40L) or B-cell antigen receptor coreceptor molecules CD19 and CD81 suffer from an antibody deficiency. Still, these patients carry low levels of memory B cells and serum antibodies.

Environmental selection and resource allocation determine spatial patterns in picophytoplankton cell size

Here we describe a new trait-based model for cellular resource allocation that we use to investigate the relative importance of different drivers for small cell size in phytoplankton. Using the model, we show that increased investment in nonscalable structural components with decreasing cell size leads to a trade-off between cell size, nutrient and light affinity, and growth rate. Within the most extreme nutrient-limited, stratified environments, resource competition theory then predicts a trend toward larger minimum cell size with increasing depth. We demonstrate that this explains observed trends using a marine ecosystem model that represents selection and adaptation of a diverse community defined by traits for cell size and subcellular resource allocation. This framework for linking cellular physiology to environmental selection can be used to investigate the adaptive response of the marine microbial community to environmental conditions and the adaptive value of variations in cellular physiology.

Simultaneous feature selection and feature weighting using Hybrid Tabu Search/K-nearest neighbor classifier

Feature selection and feature weighting are useful techniques for improving the classification accuracy of K-nearest-neighbor (K-NN) rule. The term feature selection refers to algorithms that select the best subset of the input feature set. In feature weighting, each feature is multiplied by a weight value proportional to the ability of the feature to distinguish pattern classes. In this paper, a novel hybrid approach is proposed for simultaneous feature selection and feature weighting of K-NN rule based on Tabu Search (TS) heuristic. The proposed TS heuristic in combination with K-NN classifier is compared with several classifiers on various available data sets. The results have indicated a significant improvement in the performance in classification accuracy. The proposed TS heuristic is also compared with various feature selection algorithms. Experiments performed revealed that the proposed hybrid TS heuristic is superior to both simple TS and sequential search algorithms. We also present results for the classification of prostate cancer using multispectral images, an important problem in biomedicine.

Integrated structure selection and parameter optimisation for eng-genes neural models

The eng-genes concept involves the use of fundamental known system functions as activation functions in a neural model to create a 'grey-box' neural network. One of the main issues in eng-genes modelling is to produce a parsimonious model given a model construction criterion. The challenges are that (1) the eng-genes model in most cases is a heterogenous network consisting of more than one type of nonlinear basis functions, and each basis function may have different set of parameters to be optimised; (2) the number of hidden nodes has to be chosen based on a model selection criterion. This is a mixed integer hard problem and this paper investigates the use of a forward selection algorithm to optimise both the network structure and the parameters of the system-derived activation functions. Results are included from case studies performed on a simulated continuously stirred tank reactor process, and using actual data from a pH neutralisation plant. The resulting eng-genes networks demonstrate superior simulation performance and transparency over a range of network sizes when compared to conventional neural models. (c) 2007 Elsevier B.V. All rights reserved.

Simulated predator extinctions: Predator identity affects survival and recruitment of oysters

The rate of species loss is increasing at a global scale, and human-induced extinctions are biased toward predator species. We examined the effects of predator extinctions on a foundation species, the eastern oyster (Crassostrea virginica). We performed a factorial experiment manipulating the presence and abundance of three of the most common predatory crabs, the blue crab (Callinectes sapidus), stone crab (Menippe mercenaria), and mud crab (Panopeus herbstii) in estuaries in the eastern United States. We tested the effects of species richness and identity of predators on juvenile oyster survival, oyster recruitment, and organic matter content of sediment. We also manipulated the density of each of the predators and controlled for the loss of biomass of species by maintaining a constant mass of predators in one set of treatments and simultaneously using an additive design. This design allowed us to test the density dependence of our results and test for functional compensation by other species. The identity of predator species, but not richness, affected oyster populations. The loss of blue crabs, alone or in combination with either of the other species, affected the survival rate of juvenile oysters. Blue crabs and stone crabs both affected oyster recruitment and sediment organic matter negatively. Mud crabs at higher than ambient densities, however, could fulfill some of the functions of blue and stone crabs, suggesting a level of ecological redundancy. Importantly, the strong effects of blue crabs in all processes measured no longer occurred when individuals were present at higher-than-ambient densities. Their role as dominant predator is, therefore, dependent on their density within the system and the density of other species within their guild (e.g., mud crabs). Our findings support the hypothesis that the effects of species loss at higher trophic levels are determined by predator identity and are subject to complex intraguild interactions that are largely density dependent. Understanding the role of biodiversity in ecosystem functioning or addressing practical concerns, such as loss of predators owing to overharvesting, remains complicated because accurate predictions require detailed knowledge of the system and should be drawn from sound experimental evidence, not based on observations or generalized models.

Effects of epibiotic algae on the survival, biomass and recruitment of mussels, Mytilus L. (Bivalvia : Mollusca)

Habitats composed of living 'ecosystem engineers', such as mussels, are subject to direct and indirect interactions with organisms that live among them. These interactions may affect the presence and structure of habitat, and hence, the associated taxa. We examined the direct effects of epibiotic algae on the Survival, biomass and recruitment of mussels (Mytilits L.) on the west coast of Ireland. A field experiment showed that the presence of epibiotic fucoid algae reduced the likelihood of survival of mussels during storms. We also found that the strength of attachment of mussels did not increase in the presence of epibionts. Another in situ experiment revealed that the presence of ephemeral epibiotic algal mats had no effect on the biomass of host mussels, suggesting no effect on mussel growth or production. The abundance of small mussels (