Color in scientific visualization: Perception and image-based data display

Visualization is the transformation of information into a visual display that enhances users understanding and interpretation of the data. This thesis project has investigated the use of color and human vision modeling for visualization of image-based scientific data. Two preliminary psychophysical experiments were first conducted on uniform color patches to analyze the perception and understanding of different color attributes, which provided psychophysical evidence and guidance for the choice of color space/attributes for color encoding. Perceptual color scales were then designed for univariate and bivariate image data display and their effectiveness was evaluated through three psychophysical experiments. Some general guidelines were derived for effective color scales design. Extending to high-dimensional data, two visualization techniques were developed for hyperspectral imagery. The first approach takes advantage of the underlying relationships between PCA/ICA of hyperspectral images and the human opponent color model, and maps the first three PCs or ICs to several opponent color spaces including CIELAB, HSV, YCbCr, and YUV. The gray world assumption was adopted to automatically set the mapping origins. The rendered images are well color balanced and can offer a first look capability or initial classification for a wide variety of spectral scenes. The second approach combines a true color image and a PCA image based on a biologically inspired visual attention model that simulates the center-surround structure of visual receptive fields as the difference between fine and coarse scales. The model was extended to take into account human contrast sensitivity and include high-level information such as the second order statistical structure in the form of local variance map, in addition to low-level features such as color, luminance, and orientation. It generates a topographic saliency map for both the true color image and the PCA image, a difference map is then derived and used as a mask to select interesting locations where the PCA image has more salient features than available in the visible bands. The resulting representations preserve consistent natural appearance of the scene, while the selected attentional locations may be analyzed by more advanced algorithms

How well can people use different color attributes?

Two psychophysical experiments were conducted to analyze the role of color attributes in simple tasks involving color matching and discrimination. In Experiment I observers made color matches using three different adjustment control methods. The results showed that the Lightness, Chroma, Hue (LCH) and the Lightness, redness/greenness, blueness/yellowness ({L, r/g, y/b}) adjustment controls elicited significantly better performance than the display RGB controls in terms of both accuracy and time, but were not significantly different from each other. Expert observers performed significantly better than naive observers in terms of accuracy. Experiment II was a replication and extension of Melgosa, et al.’s experiment in which observers judged differences and similarities for color attributes in pairs of colored patches. At a 95% confidence level, the results from judging difference were significantly better than those from judging similarity. Hue and Lightness were significantly more identifiable than Chroma, r/g, and y/b. For all observers, lightness differences were more easily detected for less chromatic pairs than for higher chromatic ones. With respect to the size of the color differences, it was found that larger hue differences were more easily identifiable than smaller ones. Experts could more readily identify constant lightness and chroma for large color differences while constant hue was more identifiable for small color differences. There were no significant differences found between males and females. These results indicate that people do not have ready access to the lower level color descriptors such as the common attributes used to define color spaces and that higher level psychological processing involving cognition and language may be necessary for even apparently simple tasks involving color matching and describing color differences

Perceptual Display Strategies of Hyperspectral Imagery Based on PCA and ICA

This study investigated appropriate methodologies for displaying hyperspectral imagery based on knowledge of human color vision as applied to Hyperion and AVIRIS data. Principal Component Analysis (PCA) and Independent Component Analysis (ICA) were used to reduce the data dimensionality in order to make the data more amenable to visualization in three-dimensional color space. In addition, these two methods were chosen because of their underlying relationships to the opponent color model of human color perception. PCA and ICA-based visualization strategies were then explored by mapping the first three PCs or ICs to several opponent color spaces including CIELAB, HSV, YCrCb, and YUV. The gray world assumption, which states that given an image with sufficient amount of color variations, the average color should be gray, was used to set the mapping origins. The rendered images are well color balanced and can offer a first look capability or initial classification for a wide variety of spectral scenes

Visualization of High-dimensional Remote-Sensing Data Products

This study investigated appropriate methodologies for displaying hyperspectral imagery based on knowledge of human color vision as applied to Hyperion and AVIRIS data. Principal Component Analysis (PCA) and Independent Component Analysis (ICA) were used to reduce the data dimensionality, and these two methods were chosen also because of their underlying relationships to the opponent color model of human color perception. PCA and ICA-based strategies were then explored by mapping the first three PC or IC to several opponent color spaces including CIELAB, HSV, YCbCr, and YIQ. The gray world assumption, which states that given an image with sufficient amount of color variations, the average color should be gray, was used to set the mapping origins. The rendered images are well color balanced and can offer a first look capability or initial classification for a wide variety of spectral scenes. I

Regulation of Exosomes in the Pathogenesis of Breast Cancer

Extracellular vesicles (EVs) are a heterogeneous group of endogenous nanoscale vesicles that are secreted by various cell types. Based on their biogenesis and size distribution, EVs can be broadly classified as exosomes and microvesicles. Exosomes are enveloped by lipid bilayers with a size of 30–150 nm in diameter, which contain diverse biomolecules, including lipids, proteins and nucleic acids. Exosomes transport their bioactive cargoes from original cells to recipient cells, thus play crucial roles in mediating intercellular communication. Breast cancer is the most common malignancy among women and remains a major health problem worldwide, diagnostic strategies and therapies aimed at breast cancer are still limited. Growing evidence shows that exosomes are involved in the pathogenesis of breast cancer, including tumorigenesis, invasion and metastasis. Here, we provide a straightforward overview of exosomes and highlight the role of exosomes in the pathogenesis of breast cancer, moreover, we discuss the potential application of exosomes as biomarkers and therapeutic tools in breast cancer diagnostics and therapeutics

Mucosal and Systemic Immune Responses to Influenza H7N9 Antigen HA1–2 Co-Delivered Intranasally with Flagellin or Polyethyleneimine in Mice and Chickens

Consecutive cases of human infection with H7N9 influenza viruses since 2013 in China have prompted efforts to develop an effective treatment. Subunit vaccines introduced by intranasal administration can block an infection at its primary site; flagellin (fliC) and polyethyleneimine (PEI) have been shown to be potent adjuvants. We previously generated the hemagglutinin (HA)1–2-fliC fusion protein consisting of the globular head domain (HA1–2; amino acids 62–284) of HA fused with Salmonella typhimurium fliC. In the present study, we investigated its effectiveness of both flagellin and PEI as mucosal adjuvants for the H7N9 influenza subunit vaccine. Mice immunized intranasally with HA1–2-fliC and HA1–2-PEI showed higher HA1–2-specific immunoglobulin (Ig)G and IgA titers in serum, nasal wash, and bronchial alveolar lavage fluid. Moreover, splenocyte activation and proliferation and the number of HA1–2-specific interferon (IFN)-γ- and interleukin (IL)-4-producing splenocytes were markedly increased in the fliC and PEI groups; in the latter, there were more cells secreting IL-4 than IFN-γ, suggesting that fliC induced T helper type (Th)1 and Th2 immune responses, and PEI induced Th2-biased responses, consistent with the serum antibody isotype pattern (IgG1/IgG2a ratio). Furthermore, virus challenge was performed in a chicken model. The results showed that chickens receiving fliC and PEI adjuvant vaccine exhibited robust immune responses leading to a significant reduction in viral loads of throat and cloaca compared to chickens receiving only HA1–2. These findings provide a basis for the development of H7N9 influenza HA1–2 mucosal subunit vaccines

Diagnostic Significance of Serum IgG Galactosylation in CA19-9-Negative Pancreatic Carcinoma Patients

Background: Although Carbohydrate antigen 19-9 (CA19-9) is considered clinically useful and informative for pancreatic carcinoma (PC), false positive results, and false negative results have restricted its clinical use. Especially missed or delayed diagnosis of PC patients with negative CA19-9 value limited the utility. To improve prognosis of PC patients, the discovery of reliable biomarkers to assist CA19-9 is desired. Serum IgG galactosylation based on our previous report was altered in PC patients comparing to healthy controls. The objective of this study was to explore the diagnostic significance of IgG galactosylation in assisting CA19-9 for PC in a comprehensive way.Methods: Serum IgG galactosylation profiles were analyzed by MALDI-MS in cohort 1 (n = 252) and cohort 2 in which all CA19-9 levels were negative (n = 133). In each cohort, not only healthy controls and PC patients but also benign pancreatic disease (BPD) patients were enrolled. Peaks were acquired by the software of MALDI-MS sample acquisition, followed by being processed and analyzed by the software of Progenesis MALDI. IgG Gal-ratio, which was calculated from the relative intensity of peaks G0, G1, and G2 according to the formula (G0/(G1+G2×2)), was employed as an index for indicating the distribution of IgG galactosylation.Results: The Gal-ratio was elevated in PC comparing with that in non-cancer group (healthy controls and BPD). The area under the receiver operating characteristic curve (AUC) of IgG Gal-ratio was higher than that of CA19-9 (0.912 vs. 0.814). The performance was further improved when Gal-ratio and CA19-9 were combined (AUC: 0.928). Meanwhile, Gal-ratio also had great diagnostic value with a sensitivity of 92.31% (AUC: 0.883) in detection of PC at early stage. Notably, IgG Gal-ratio has great sensitivity (90.63%) and specificity (76.81%) in CA19-9-negative PC patients.Conclusions: IgG Gal-ratio had a great performance in detection of PC and could be used to assist CA19-9 in improving diagnosis performance through early stage detection, differentiation from BPD, and PC diagnosis with CA19-9-negative level

Microbial-environmental interactions reveal the evaluation of fermentation time on the nutrient properties of soybean meal

Microbial fermentation techniques are often used to improve their quality, where the keys are fermentation strains and fermentation time. This study studied the interaction between microbiota and environmental (or nutritional) factors and microbiota at different fermentation times to determine the most appropriate time, using lactic acid bacteria as fermentation strains. It can be concluded that fermentation improved the nutritional value of soybean meals. In the early stages of fermentation, debris in soybean meal highly proliferated and destabilized the microbial community, while pH and nutritional conditions played an important role in helping its stabilization. In addition, we must pay attention to the interspecific interactions of microorganisms, which makes it easy to understand how the microbial community maintains community stability. A 4-day fermentation of soybean meal with Lactobacillus is recommended