Hierarchical Cluster Analysis to Aid Diagnostic Image Data Visualization of MS and Other Medical Imaging Modalities

Perceiving abnormal regions in the images of different medical modalities plays a crucial role in diagnosis and subsequent treatment planning. In medical images to visually perceive abnormalities’ extent and boundaries requires substantial experience. Consequently, manually drawn region of interest (ROI) to outline boundaries of abnormalities suffers from limitations of human perception leading to inter-observer variability. As an alternative to human drawn ROI, it is proposed the use of a computer-based segmenta- tion algorithm to segment digital medical image data. Hierarchical Clustering-based Segmentation (HCS) process is a generic unsupervised segmentation process that can be used to segment dissimilar regions in digital images. HCS process generates a hierarchy of segmented images by partitioning an image into its constituent regions at hierarchical levels of allowable dissimilarity between its different regions. The hierarchy represents the continuous merging of similar, spatially adjacent, and/or disjoint regions as the allowable threshold value of dissimilarity between regions, for merging, is gradually increased. This chapter discusses in detail first the implementation of the HCS process, second the implementa- tion details of how the HCS process is used for the presentation of multi-modal imaging data (MALDI and MRI) of a biological sample, third the implementation details of how the process is used as a perception aid for X-ray mammogram readers, and finally the implementation details of how it is used as an interpreta- tion aid for the interpretation of Multi-parametric Magnetic Resonance Imaging (mpMRI) of the Prostate

Regional differences in APD restitution can initiate wavebreak and re-entry in cardiac tissue: A computational study

Background Regional differences in action potential duration (APD) restitution in the heart favour arrhythmias, but the mechanism is not well understood. Methods We simulated a 150 × 150 mm 2D sheet of cardiac ventricular tissue using a simplified computational model. We investigated wavebreak and re-entry initiated by an S1S2S3 stimulus protocol in tissue sheets with two regions, each with different APD restitution. The two regions had a different APD at short diastolic interval (DI), but similar APD at long DI. Simulations were performed twice; once with both regions having steep (slope > 1), and once with both regions having flat (slope < 1) APD restitution. Results Wavebreak and re-entry were readily initiated using the S1S2S3 protocol in tissue sheets with two regions having different APD restitution properties. Initiation occurred irrespective of whether the APD restitution slopes were steep or flat. With steep APD restitution, the range of S2S3 intervals resulting in wavebreak increased from 1 ms with S1S2 of 250 ms, to 75 ms (S1S2 180 ms). With flat APD restitution, the range of S2S3 intervals resulting in wavebreak increased from 1 ms (S1S2 250 ms), to 21 ms (S1S2 340 ms) and then 11 ms (S1S2 400 ms). Conclusion Regional differences in APD restitution are an arrhythmogenic substrate that can be concealed at normal heart rates. A premature stimulus produces regional differences in repolarisation, and a further premature stimulus can then result in wavebreak and initiate re-entry. This mechanism for initiating re-entry is independent of the steepness of the APD restitution curve

Quantification of tumour vasculature and hypoxia by immunohistochemical staining and HbO2 saturation measurements

Despite the possibility that tumour hypoxia may limit radiotherapeutic response, the underlying mechanisms remain poorly understood. A new methodology has been developed in which information from several sophisticated techniques is combined and analysed at a microregional level. First, tumour oxygen availability is spatially defined by measuring intravascular blood oxygen saturations (HbO2) cryospectrophotometrically in frozen tumour blocks. Second, hypoxic development is quantified in adjacent sections using immunohistochemical detection of a fluorescently conjugated monoclonal antibody (ELK3-51) to a nitroheterocyclic hypoxia marker (EF5), thereby providing information relating to both the oxygen consumption rates and the effective oxygen diffusion distances. Third, a combination of fluorescent (Hoechst 33342 or DiOC7(3)) and immunohistological (PECAM-1/CD31) stains is used to define the anatomical vascular densities and the fraction of blood vessels containing flow. Using a computer-interfaced microscope stage, image analysis software and a 3-CCD colour video camera, multiple images are digitized, combined to form a photo-montage and revisited after each of the three staining protocols. By applying image registration techniques, the spatial distribution of HbO2 saturations is matched to corresponding hypoxic marker intensities in adjacent sections. This permits vascular configuration to be related to oxygen availability and allows the hypoxic marker intensities to be quantitated in situ. © 1999 Cancer Research Campaig

Primary source of income is associated with differences in HIV risk behaviors in street-recruited samples

BACKGROUND: The relationship between primary source of income and HIV risk behaviors and the racial/ethnic differences in risk behavior profiles among disadvantaged populations have not been fully explored. This is unusual given that the phenomenon of higher risk in more disadvantaged populations is well-known but the mechanisms remain unclear. We examined the relationship between primary source of income and differences in HIV risk behaviors among four racial/ethnic groups in the southern United States. METHODS: Self-reported data on primary source of income and HIV risk behaviors were collected from 1494 African American, Hispanic, Asian, and White men and women in places of public congregation in Houston, Texas. Data were analyzed using calculation of percentages and by chi-square tests with Yates correction for discontinuity where appropriate. RESULTS: Data revealed that a higher proportion of whites were involved in sex for money exchanges compared to the other racial groups in this sample. The data suggest that similar street sampling approaches are likely to recruit different proportions of people by primary income source and by ethnicity. It may be that the study locations sampled are likely to preferentially attract those involved in illegal activities, specifically the white population involved in sex for drug or money exchanges. Research evidence has shown that people construct highly evolved sexual marketplaces that are localized and most unlikely to cross racial, ethnic, and socioeconomic or geographical boundaries. Thus, the areas that we sampled may have straddled a white sexual marketplace more than that of the other groups, leading to an over-representation of sex exchange in this group. Drug use was highest among those with illegal primary sources of income (sex exchange and drug dealing and theft), and they were also those most likely to have injected drugs rather than administered them by any other route (p < 0.001). In addition, bisexual or homosexual identification was reported by more respondents in the sex exchange as primary source of income category. The number of sexual partners in the last three months followed a similar pattern, with those whose primary source of income was drug dealing or theft reporting relatively high partner numbers. CONCLUSIONS: These data suggest that social disadvantage is associated with HIV risk in part by its association with drug and sex work for survival, and offers one variable that may be associated with the concentration of disease among those at greatest disadvantage by having an illegal and unstable primary income source

Incentive or Habit Learning in Amphibians?

Toads (Rhinella arenarum) received training with a novel incentive procedure involving access to solutions of different NaCl concentrations. In Experiment 1, instrumental behavior and weight variation data confirmed that such solutions yield incentive values ranging from appetitive (deionized water, DW, leading to weight gain), to neutral (300 mM slightly hypertonic solution, leading to no net weight gain or loss), and aversive (800 mM highly hypertonic solution leading to weight loss). In Experiment 2, a downshift from DW to a 300 mM solution or an upshift from a 300 mM solution to DW led to a gradual adjustment in instrumental behavior. In Experiment 3, extinction was similar after acquisition with access to only DW or with a random mixture of DW and 300 mM. In Experiment 4, a downshift from DW to 225, 212, or 200 mM solutions led again to gradual adjustments. These findings add to a growing body of comparative evidence suggesting that amphibians adjust to incentive shifts on the basis of habit formation and reorganization

Low Mate Encounter Rate Increases Male Risk Taking in a Sexually Cannibalistic Praying Mantis

Male praying mantises are forced into the ultimate trade-off of mating versus complete loss of future reproduction if they fall prey to a female. The balance of this trade-off will depend both on (1) the level of predatory risk imposed by females and (2) the frequency of mating opportunities for males. We report the results of a set of experiments that examine the effects of these two variables on male risk-taking behavior and the frequency of sexual cannibalism in the praying mantis Tenodera sinensis. We experimentally altered the rate at which males encountered females and measured male approach and courtship behavior under conditions of high and low risk of being attacked by females. We show that male risk taking depends on prior access to females. Males with restricted access to females showed greater risk-taking behavior. When males were given daily female encounters, they responded to greater female-imposed risk by slowing their rate of approach and remained a greater distance from a potential mate. In contrast, males without recent access to mates were greater risk-takers; they approached females more rapidly and to closer proximity, regardless of risk. In a second experiment, we altered male encounter rate with females and measured rates of sexual cannibalism when paired with hungry or well-fed females. Greater risk-taking behavior by males with low mate encounter rates resulted in high rates of sexual cannibalism when these males were paired with hungry females

Ensemble Composition and Activity Levels of Insectivorous Bats in Response to Management Intensification in Coffee Agroforestry Systems

Shade coffee plantations have received attention for their role in biodiversity conservation. Bats are among the most diverse mammalian taxa in these systems; however, previous studies of bats in coffee plantations have focused on the largely herbivorous leaf-nosed bats (Phyllostomidae). In contrast, we have virtually no information on how ensembles of aerial insectivorous bats – nearly half the Neotropical bat species – change in response to habitat modification. To evaluate the effects of agroecosystem management on insectivorous bats, we studied their diversity and activity in southern Chiapas, Mexico, a landscape dominated by coffee agroforestry. We used acoustic monitoring and live captures to characterize the insectivorous bat ensemble in forest fragments and coffee plantations differing in the structural and taxonomic complexity of shade trees. We captured bats of 12 non-phyllostomid species; acoustic monitoring revealed the presence of at least 12 more species of aerial insectivores. Richness of forest bats was the same across all land-use types; in contrast, species richness of open-space bats increased in low shade, intensively managed coffee plantations. Conversely, only forest bats demonstrated significant differences in ensemble structure (as measured by similarity indices) across land-use types. Both overall activity and feeding activity of forest bats declined significantly with increasing management intensity, while the overall activity, but not feeding activity, of open-space bats increased. We conclude that diverse shade coffee plantations in our study area serve as valuable foraging and commuting habitat for aerial insectivorous bats, and several species also commute through or forage in low shade coffee monocultures

Location of Pathogenic Bacteria during Persistent Infections: Insights from an Analysis Using Game Theory

Bacterial persistent infections are responsible for a significant amount of the human morbidity and mortality. Unlike acute bacterial infections, it is very difficult to treat persistent bacterial infections (e.g. tuberculosis). Knowledge about the location of pathogenic bacteria during persistent infection will help to treat such conditions by designing novel drugs which can reach such locations. In this study, events of bacterial persistent infections were analyzed using game theory. A game was defined where the pathogen and the host are the two players with a conflict of interest. Criteria for the establishment of Nash equilibrium were calculated for this game. This theoretical model, which is very simple and heuristic, predicts that during persistent infections pathogenic bacteria stay in both intracellular and extracellular compartments of the host. The result of this study implies that a bacterium should be able to survive in both intracellular and extracellular compartments of the host in order to cause persistent infections. This explains why persistent infections are more often caused by intracellular pathogens like Mycobacterium and Salmonella. Moreover, this prediction is in consistence with the results of previous experimental studies

Ensemble Composition and Activity Levels of Insectivorous Bats in Response to Management Intensification in Coffee Agroforestry Systems

Shade coffee plantations have received attention for their role in biodiversity conservation. Bats are among the most diverse mammalian taxa in these systems; however, previous studies of bats in coffee plantations have focused on the largely herbivorous leaf-nosed bats (Phyllostomidae). In contrast, we have virtually no information on how ensembles of aerial insectivorous bats – nearly half the Neotropical bat species – change in response to habitat modification. To evaluate the effects of agroecosystem management on insectivorous bats, we studied their diversity and activity in southern Chiapas, Mexico, a landscape dominated by coffee agroforestry. We used acoustic monitoring and live captures to characterize the insectivorous bat ensemble in forest fragments and coffee plantations differing in the structural and taxonomic complexity of shade trees. We captured bats of 12 non-phyllostomid species; acoustic monitoring revealed the presence of at least 12 more species of aerial insectivores. Richness of forest bats was the same across all land-use types; in contrast, species richness of open-space bats increased in low shade, intensively managed coffee plantations. Conversely, only forest bats demonstrated significant differences in ensemble structure (as measured by similarity indices) across land-use types. Both overall activity and feeding activity of forest bats declined significantly with increasing management intensity, while the overall activity, but not feeding activity, of open-space bats increased. We conclude that diverse shade coffee plantations in our study area serve as valuable foraging and commuting habitat for aerial insectivorous bats, and several species also commute through or forage in low shade coffee monocultures