Neural-network-based classification of cognitively normal, demented, Alzheimer disease and vascular dementia from single photon emission with computed tomography image data from brain.

Single photon emission with computed tomography (SPECT) hexamethylphenylethyleneamineoxime technetium-99 images were analyzed by an optimal interpolative neural network (OINN) algorithm to determine whether the network could discriminate among clinically diagnosed groups of elderly normal, Alzheimer disease (AD), and vascular dementia (VD) subjects. After initial image preprocessing and registration, image features were obtained that were representative of the mean regional tissue uptake. These features were extracted from a given image by averaging the intensities over various regions defined by suitable masks. After training, the network classified independent trials of patients whose clinical diagnoses conformed to published criteria for probable AD or probable/possible VD. For the SPECT data used in the current tests, the OINN agreement was 80 and 86% for probable AD and probable/possible VD, respectively. These results suggest that artificial neural network methods offer potential in diagnoses from brain images and possibly in other areas of scientific research where complex patterns of data may have scientifically meaningful groupings that are not easily identifiable by the researcher.

Evidence for reciprocal antagonism between motion sensors tuned to coarse and fine features

Early visual processing analyses fine and coarse image features separately. Here we show that motion signals derived from fine and coarse analyses are combined in rather a surprising way: Coarse and fine motion sensors representing the same direction of motion inhibit one another and an imbalance can reverse the motion perceived. Observers judged the direction of motion of patches of filtered two-dimensional noise, centered on 1 and 3 cycles/deg. When both sets of noise were present and only the 3 cycles/deg noise moved, judgments were reversed at short durations. When both sets of noise moved, judgments were correct but sensitivity was impaired. Reversals and impairments occurred both with isotropic noise and with orientation-filtered noise. The reversals and impairments could be simulated in a model of motion sensing by adding a stage in which the outputs of motion sensors tuned to 1 and 3 cycles/deg and the same direction of motion were subtracted from one another. The subtraction model predicted and we confirmed in experiments with orientation-filtered noise that if the 1 cycle/deg noise flickered and the 3 cycles/deg noise moved, the 1 cycle/deg noise appeared to move in the opposite direction to the 3 cycles/deg noise even at long durations.

The effect of inversion on the encoding of normal and “thatcherized” faces

In the "Thatcher illusion" a face, in which the eyes and mouth are inverted relative to the rest of the face, looks grotesque when shown upright but not when inverted. In four experiments we investigated the contribution of local and global processing to this illusion in normal observers. We examined inversion effects (i.e., better performance for upright than for inverted faces) in a task requiring discrimination of whether faces were or were not "thatcherized". Observers made same/different judgements to isolated face parts (Experiments 1-2) and to whole faces (Experiments 3-4). Face pairs had the same or different identity, allowing for different processing strategies using feature-based or configural information, respectively. In Experiment 1, feature-based matching of same-person face parts yielded only a small inversion effect for normal face parts. However, when feature-based matching was prevented by using the face parts of different people on all trials (Experiment 2) an inversion effect occurred for normal but not for thatcherized parts. In Experiments 3 and 4, inversion effects occurred with normal but not with thatcherized whole faces, on both same- and different-person matching tasks. This suggests that a common configural strategy was used with whole (normal) faces. Face context facilitated attention to misoriented parts in same-person but not in different-person matching. The results indicate that (1) face inversion disrupts local configural processing, but not the processing of image features, and (2) thatcherization disrupts local configural processing in upright faces.

Petrographic image analysis and understanding

This study considers the application of image analysis in petrography and investigates the possibilities for advancing existing techniques by introducing feature extraction and analysis capabilities of a higher level than those currently employed. The aim is to construct relevant, useful descriptions of crystal form and inter-crystal relations in polycrystalline igneous rock sections. Such descriptions cannot be derived until the `ownership' of boundaries between adjacent crystals has been established: this is the fundamental problem of crystal boundary assignment. An analysis of this problem establishes key image features which reveal boundary ownership; a set of explicit analysis rules is presented. A petrographic image analysis scheme based on these principles is outlined and the implementation of key components of the scheme considered. An algorithm for the extraction and symbolic representation of image structural information is developed. A new multiscale analysis algorithm which produces a hierarchical description of the linear and near-linear structure on a contour is presented in detail. Novel techniques for symmetry analysis are developed. The analyses considered contribute both to the solution of the boundary assignment problem and to the construction of geologically useful descriptions of crystal form. The analysis scheme which is developed employs grouping principles such as collinearity, parallelism, symmetry and continuity, so providing a link between this study and more general work in perceptual grouping and intermediate level computer vision. Consequently, the techniques developed in this study may be expected to find wider application beyond the petrographic domain.

Can mean shift trackers perform better?

Many tracking algorithms have difficulties dealing with occlusions and background clutters, and consequently don't converge to an appropriate solution. Tracking based on the mean shift algorithm has shown robust performance in many circumstances but still fails e.g. when encountering dramatic intensity or colour changes in a pre-defined neighbourhood. In this paper, we present a robust tracking algorithm that integrates the advantages of mean shift tracking with those of tracking local invariant features. These features are integrated into the mean shift formulation so that tracking is performed based both on mean shift and feature probability distributions, coupled with an expectation maximisation scheme. Experimental results show robust tracking performance on a series of complicated real image sequences. © 2010 IEEE.

Content-aware approach for improving biomedical image analysis: an interdisciplinary study series

Biomedicine is a highly interdisciplinary research area at the interface of sciences, anatomy, physiology, and medicine. In the last decade, biomedical studies have been greatly enhanced by the introduction of new technologies and techniques for automated quantitative imaging, thus considerably advancing the possibility to investigate biological phenomena through image analysis. However, the effectiveness of this interdisciplinary approach is bounded by the limited knowledge that a biologist and a computer scientist, by professional training, have of each other’s fields. The possible solution to make up for both these lacks lies in training biologists to make them interdisciplinary researchers able to develop dedicated image processing and analysis tools by exploiting a content-aware approach. The aim of this Thesis is to show the effectiveness of a content-aware approach to automated quantitative imaging, by its application to different biomedical studies, with the secondary desirable purpose of motivating researchers to invest in interdisciplinarity. Such content-aware approach has been applied firstly to the phenomization of tumour cell response to stress by confocal fluorescent imaging, and secondly, to the texture analysis of trabecular bone microarchitecture in micro-CT scans. Third, this approach served the characterization of new 3-D multicellular spheroids of human stem cells, and the investigation of the role of the Nogo-A protein in tooth innervation. Finally, the content-aware approach also prompted to the development of two novel methods for local image analysis and colocalization quantification. In conclusion, the content-aware approach has proved its benefit through building new approaches that have improved the quality of image analysis, strengthening the statistical significance to allow unveiling biological phenomena. Hopefully, this Thesis will contribute to inspire researchers to striving hard for pursuing interdisciplinarity.

The ichthyofauna of upper rio Capivari: defining conservation strategies based on the composition and distribution of fish species

Although the rio Capivari basin is recognized as an area of great importance for the ichthyofauna, it lacks virtually every basic requirement for the definition of appropriate conservation strategies, since not even its species composition is known. The objective of this work is to determine the composition and distribution of fish species in the upper rio Capivari basin, relating them to the local physical features, and to evaluate the effectiveness of proposed conservations units, delimited based on areas of native vegetation remains, on the conservation of local ichthyofauna. During 2007, 50 different watercourses were sampled with gillnets, cast nets and kick nets. A total of 1308 individuals belonging to 41 species were captured. Degree of conservation, altitude and width were the parameters that best explained fish species richness. Considering the recently proposed boundaries for potential conservation units in the region only 15 or 20 out of 41 species would be found in the State Park and Environmental Protection Area respectively. In practice, the proposed conservation units would not be effective tools for fish conservation, since it would be located in mountainous areas of high altitude, of headwaters streams and where few species are found. In such context, the conservation of specific stretches of larger rivers is critical.

Automatic Network Fingerprinting through Single-Node Motifs

Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs-a combination of local network features. One technique to identify single node-motifs has been presented by Costa et al. (L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009). Here, we first suggest improvements to the method including how its parameters can be determined automatically. Such automatic routines make high-throughput studies of many networks feasible. Second, the new routines are validated in different network-series. Third, we provide an example of how the method can be used to analyse network time-series. In conclusion, we provide a robust method for systematically discovering and classifying characteristic nodes of a network. In contrast to classical motif analysis, our approach can identify individual components (here: nodes) that are specific to a network. Such special nodes, as hubs before, might be found to play critical roles in real-world networks.

Immune responses in hookworm infections

Hookworms infect perhaps one-fifth of the entire human population, yet little is known about their interaction with our immune system. The two major species are Necator americanus, which is adapted to tropical conditions, and Ancylostoma duodenale, which predominates in more temperate zones. While having many common features, they also differ in several key aspects of their biology. Host immune responses are triggered by larval invasion of the skin, larval migration through the circulation and lungs, and worm establishment in the intestine, where adult worms feed on blood and mucosa while injecting various molecules that facilitate feeding and modulate host protective responses. Despite repeated exposure, protective immunity does not seem to develop in humans, so that infections occur in all age groups (depending on exposure patterns) and tend to be prolonged. Responses to both larval and adult worms have a characteristic T-helper type 2 profile, with activated mast cells in the gut mucosa, elevated levels of circulating immunoglobulin E, and eosinoophilia in the peripheral blood and local tissues, features also characteristic of type I hypersensitivity reactions. The longevity of adult hookworms is determined probably more by parasite genetics than by host immunity. However, many of the proteins released by the parasites seem to have immunomodulatory activity, presumably for self-protection. Advances in molecular biotechnology enable the identification and characterization of increasing numbers of these parasite molecules and should enhance our detailed understanding of the protective and pathogenetic mechanisms in hookworm infections.

Segmentation of striatal brain structures from high resolution pet images

Dissertation presented at the Faculty of Science and Technology of the New University of Lisbon in fulfillment of the requirements for the Masters degree in Electrical Engineering and Computers

Estrutura a partir do Movimento em Sistemas Autónomos

Mestrado em Engenharia Electrotécnica e de Computadores - Ramo de Sistemas Autónomos

Long-term outcomes of school-based treatment for control of urinary schistosomiasis: a review of experience in Coast Province, Kenya

Urinary schistosomiasis remains a significant burden for Africa and the Middle East. The success of population-based control programs will depend on their impact, over many years, on Schistosoma haematobium reinfection and associated disease. In a multi-year (1984-1992) control program in Kenya, we examined risk for S. haematobium reinfection and late disease during and after annual school-based treatment. In this setting, long-term risk of new infection was independently associated with location, age, hematuria, and incomplete treatment, but not with sex or frequency of water contact. Thus, very local environmental features and age-related factors played an important role in S. haematobium transmission, such that population-based control programs should optimally tailor their efforts to local conditions on a village-by-village basis. In 2001-2002, the late benefits of earlier participation in school-based antischistosomal therapy were estimated in a cohort of formerly-treated adult residents compared to never-treated adults from the same villages. Among age-matched subjects, current infection prevalence was lower among those who had received remote therapy. In addition, prevalence of bladder abnormality was lower in the treated group, who were free of severe bladder disease. Treatment of affected adults resulted in rapid resolution of infection and any detectable bladder abnormalities. We conclude that continued treatment into adulthood, as well as efforts at long-term prevention of infection (transmission control) are necessary to achieve optimal morbidity control in affected communities.

Online Robust 3D Mapping Using Structure from Motion Cues

This paper presents a complete solution for creating accurate 3D textured models from monocular video sequences. The methods are developed within the framework of sequential structure from motion, where a 3D model of the environment is maintained and updated as new visual information becomes available. The camera position is recovered by directly associating the 3D scene model with local image observations. Compared to standard structure from motion techniques, this approach decreases the error accumulation while increasing the robustness to scene occlusions and feature association failures. The obtained 3D information is used to generate high quality, composite visual maps of the scene (mosaics). The visual maps are used to create texture-mapped, realistic views of the scene

Identification of geometrically consistent interest points for 3D scene reconstruction

We propose an algorithm that extracts image features that are consistent with the 3D structure of the scene. The features can be robustly tracked over multiple views and serve as vertices of planar patches that suitably represent scene surfaces, while reducing the redundancy in the description of 3D shapes. In other words, the extracted features will off er good tracking properties while providing the basis for 3D reconstruction with minimum model complexity

Comparison of hospital-wide and unit-specific cumulative antibiograms in hospital- and community-acquired infection.

BACKGROUND: Empirical antibacterial therapy in hospitals is usually guided by local epidemiologic features reflected by institutional cumulative antibiograms. We investigated additional information inferred by aggregating cumulative antibiograms by type of unit or according to the place of acquisition (i.e. community vs. hospital) of the bacteria. MATERIALS AND METHODS: Antimicrobial susceptibility rates of selected pathogens were collected over a 4-year period in an university-affiliated hospital. Hospital-wide antibiograms were compared with those selected by type of unit and sampling time (<48 or >48 h after hospital admission). RESULTS: Strains isolated >48 h after admission were less susceptible than those presumably arising from the community (<48 h). The comparison of units revealed significant differences among strains isolated >48 h after admission. When compared to hospital-wide antibiograms, susceptibility rates were lower in the ICU and surgical units for Escherichia coli to amoxicillin-clavulanate, enterococci to penicillin, and Pseudomonas aeruginosa to anti-pseudomonal beta-lactams, and in medical units for Staphylococcus aureus to oxacillin. In contrast, few differences were observed among strains isolated within 48 h of admission. CONCLUSIONS: Hospital-wide antibiograms reflect the susceptibility pattern for a specific unit with respect to community-acquired, but not to hospital-acquired strains. Antibiograms adjusted to these parameters may be useful in guiding the choice of empirical antibacterial therapy.