Embedding Spatial Software Visualization in the IDE: an Exploratory Study

Software visualization can be of great use for understanding and exploring a software system in an intuitive manner. Spatial representation of software is a promising approach of increasing interest. However, little is known about how developers interact with spatial visualizations that are embedded in the IDE. In this paper, we present a pilot study that explores the use of Software Cartography for program comprehension of an unknown system. We investigated whether developers establish a spatial memory of the system, whether clustering by topic offers a sound base layout, and how developers interact with maps. We report our results in the form of observations, hypotheses, and implications. Key findings are a) that developers made good use of the map to inspect search results and call graphs, and b) that developers found the base layout surprising and often confusing. We conclude with concrete advice for the design of embedded software maps

Microscopic Picture of Aging in SiO2

We investigate the aging dynamics of amorphous SiO2 via molecular dynamics simulations of a quench from a high temperature Ti to a lower temperature Tf.We obtain a microscopic picture of aging dynamics by analyzing single particle trajectories, identifying jump events when a particle escapes the cage formed by its neighbors, and determining how these jumps depend on the waiting time tw, the time elapsed since the temperature quench to Tf. We find that the only tw-dependent microscopic quantity is the number of jumping particles per unit time, which decreases with age. Similar to previous studies for fragile glass formers, we show here for the strong glass former SiO2 that neither the distribution of jump lengths nor the distribution of times spent in the cage are tw dependent.We conclude that the microscopic aging dynamics is surprisingly similar for fragile and strong glass formers.

A Kinetostatic Formulation for Load-Flow Visualization in Compliant Mechanisms

Load flow visualization, which is an important step in structural and machine assembly design may aid in the analysis and eventual synthesis of compliant mechanisms. In this paper, we present a kineto-static formulation to visualize load flow in compliant mechanisms. This formulation uses the concept of transferred forces to quantify load flow from input to the output of a compliant mechanism. The magnitude and direction of load flow in the constituent members enables functional decomposition of the compliant mechanism into (i) Constraints (C): members that are constrained to deform in a particular direction and (ii) Transmitters (T): members that transmit load to the output. Furthermore, it is shown that a constraint member and an adjacent transmitter member can be grouped together to constitute a fundamental building block known as an CT set whose load flow behavior is maximally decoupled from the rest of the mechanism. We can thereby explain the deformation behavior of a number of compliant mechanisms from literature by visualizing load flow, and identifying building blocks.

Characterization of vascular cavity coatings and microscopic tube-shaped structures from Upper Cretaceous dinosaur bone: evidence of a bacterial origin for dinosaur blood vessels""

Recent claims of blood vessels extracted from dinosaur fossils challenge classical views of soft-tissue preservation. Alternatively, these structures may represent postdepositional,diagenetic biofilms that grew on vascular cavity surfaces within the fossil. Similar red, hollow, tube-shaped structures were recovered from well-preserved and poorly-preserved (abraded, desiccated, exposed) Upper Cretaceous dinosaur fossils in this study. Integration of light microscopy, scanning electron microscopy, and energy dispersive x-ray spectroscopy was used to compare these vessel structures to the fossils from which they are derived. Vessel structures are typically 100-400 μm long, 0.5-1.5 μm thick, 10-40 μm in diameter and take on a wide range of straight, curved, andbranching morphologies. Interior surfaces vary from smooth to globular and typically contain spheres, rods, and fibrous structures (< 2 μm in diameter) incorporated into the surface. Exterior surfaces exhibit 2-μm-tall converging ridges, spaced 1-3 μm apart, that are sub-parallel to the long axis of the vessel structure. Fossil vascular cavities are typically coated with a smooth or grainy orange layer that shows a wide range of textures including smooth, globular, rough, ropy, and combinations thereof. Coatings tend to overlay secondary mineral crystals and framboids, confirming they are not primary structures of the fossil. For some cavity coatings, the surface that had been in contact with the bone exhibits a ridged texture, similar to that of vessel structures, having formed as a mold of the intravascular bone surface. Thus, vessel structures are interpreted as intact cavity coatings isolated after the fossil is demineralized. The presence of framboids and structures consistent in size and shape with bacteria cells, the abundance of iron in cavity coatings, and the growth of biofilms directly from the fossil that resemble respective cavity coatings support the hypothesis that vessel structures result from ironconsuming bacteria that form biofilms on the intravascular bone surfaces of fossil dinosaur bone. This also accounts for microstructures resembling osteocytes as some fossil lacunae are filled with the same iron oxide that comprises vessel structures andcoatings. Results of this study show that systematic, high-resolution SEM analyses of vertebrate fossils can provide improved insight on microtaphonomic processes, including the role of bacteria in diagenesis. These results conflict with earlier claims of dinosaurblood vessels and osteocytes.

Dual-energy CT-cholangiography in potential donors for living-related liver transplantation: Improved biliary visualization by intravenous morphine co-medication

PURPOSE: To prospectively evaluate whether intravenous morphine co-medication improves bile duct visualization of dual-energy CT-cholangiography. MATERIALS AND METHODS: Forty potential donors for living-related liver transplantation underwent CT-cholangiography with infusion of a hepatobiliary contrast agent over 40min. Twenty minutes after the beginning of the contrast agent infusion, either normal saline (n=20 patients; control group [CG]) or morphine sulfate (n=20 patients; morphine group [MG]) was injected. Forty-five minutes after initiation of the contrast agent, a dual-energy CT acquisition of the liver was performed. Applying dual-energy post-processing, pure iodine images were generated. Primary study goals were determination of bile duct diameters and visualization scores (on a scale of 0 to 3: 0-not visualized; 3-excellent visualization). RESULTS: Bile duct visualization scores for second-order and third-order branch ducts were significantly higher in the MG compared to the CG (2.9±0.1 versus 2.6±0.2 [P<0.001] and 2.7±0.3 versus 2.1±0.6 [P<0.01], respectively). Bile duct diameters for the common duct and main ducts were significantly higher in the MG compared to the CG (5.9±1.3mm versus 4.9±1.3mm [P<0.05] and 3.7±1.3mm versus 2.6±0.5mm [P<0.01], respectively). CONCLUSION: Intravenous morphine co-medication significantly improved biliary visualization on dual-energy CT-cholangiography in potential donors for living-related liver transplantation.

Postreperfusion cardiac arrest and resuscitation during orthotopic liver transplantation: dynamic visualization and analysis of physiologic recordings

We recently reported on the Multi Wave Animator (MWA), a novel open-source tool with capability of recreating continuous physiologic signals from archived numerical data and presenting them as they appeared on the patient monitor. In this report, we demonstrate for the first time the power of this technology in a real clinical case, an intraoperative cardiopulmonary arrest following reperfusion of a liver transplant graft. Using the MWA, we animated hemodynamic and ventilator data acquired before, during, and after cardiac arrest and resuscitation. This report is accompanied by an online video that shows the most critical phases of the cardiac arrest and resuscitation and provides a basis for analysis and discussion. This video is extracted from a 33-min, uninterrupted video of cardiac arrest and resuscitation, which is available online. The unique strength of MWA, its capability to accurately present discrete and continuous data in a format familiar to clinicians, allowed us this rare glimpse into events leading to an intraoperative cardiac arrest. Because of the ability to recreate and replay clinical events, this tool should be of great interest to medical educators, researchers, and clinicians involved in quality assurance and patient safety.

Visualization Techniques For The Analysis Of Network Simulation Results

The Simulation Automation Framework for Experiments (SAFE) streamlines the de- sign and execution of experiments with the ns-3 network simulator. SAFE ensures that best practices are followed throughout the workflow a network simulation study, guaranteeing that results are both credible and reproducible by third parties. Data analysis is a crucial part of this workflow, where mistakes are often made. Even when appearing in highly regarded venues, scientific graphics in numerous network simulation publications fail to include graphic titles, units, legends, and confidence intervals. After studying the literature in network simulation methodology and in- formation graphics visualization, I developed a visualization component for SAFE to help users avoid these errors in their scientific workflow. The functionality of this new component includes support for interactive visualization through a web-based interface and for the generation of high-quality, static plots that can be included in publications. The overarching goal of my contribution is to help users create graphics that follow best practices in visualization and thereby succeed in conveying the right information about simulation results.

Microscopic and Spectroscopic Methods for Probing the Clay Water Interface

Clay minerals have a fundamental importance in many processes in soils and sediments such as the bioavailability of nutrients, water retention, the adsorption of common pollutants, and the formation of an impermeable barrier upon swelling. Many of the properties of clay minerals are due to the unique environment present at the clay mineral/water interface. Traditional techniques such as X-ray diffraction (XRD) and absorption isotherms have provided a wealth of information about this interface but have suffered from limitations. The methods and results presented herein are designed to yield new experimental information about the clay mineral/water interface.A new method of studying the swelling dynamics of clay minerals was developed using in situ atomic force microscopy (AFM). The preliminary results presented here demonstrate that this technique allows one to study individual clay mineral unit layers, explore the natural heterogeneities of samples, and monitor swelling dynamics of clay minerals in real time. Cation exchange experiments were conducted monitoring the swelling change of individual nontronite quasi-crystals as the chemical composition of the surrounding environment was manipulated several times. A proof of concept study has shown that the changes in swelling are from the exchange of interlayer cations and not from the mechanical force of replacing the solution in the fluid cell. A series of attenuated total internal reflection Fourier transform infrared spectroscopy (ATR-FTIR) experiments were performed to gain a better understanding of the organization of water within the interlayer region of two Fe-bearing clay minerals. These experiments made use of the Subtractive Kramers-Kronig (SKK) Transform and the calculation of difference spectra to obtain information about interfacial water hidden within the absorption bands of bulk water. The results indicate that the reduction of structural iron disrupts the organization of water around a strongly hydrated cation such as sodium as the cation transitions from an outer-sphere complex with the mineral surface to an inner-sphere complex. In the case of a less strongly hydrated cation such as potassium, reduction of structural iron actually increases the ordering of water molecules at the mineral surface. These effects were only noticed with the reduction of iron in the tetrahedral sheet close to the basal surface where the increased charge density is localized closer to the cations in the interlayer.

Interaction of fine particles and nanoparticles with red blood cells visualized with advanced microscopic techniques

So far, little is known about the interaction of nanoparticles with lung cells, the entering of nanoparticles, and their transport through the blood stream to other organs. The entering and localization of different nanoparticles consisting of differing materials and of different charges were studied in human red blood cells. As these cells do not have any phagocytic receptors on their surface, and no actinmyosin system, we chose them as a model for nonphagocytic cells to study how nanoparticles penetrate cell membranes. We combined different microscopic techniques to visualize fine and nanoparticles in red blood cells: (I) fluorescent particles were analyzed by laser scanning microscopy combined with digital image restoration, (II) gold particles were analyzed by conventional transmission electron microscopy and energy filtering transmission electron microscopy, and (III) titanium dioxide particles were analyzed by energy filtering transmission electron microscopy. By using these differing microscopic techniques we were able to visualize and detect particles < or = 0.2 microm and nanoparticles in red blood cells. We found that the surface charge and the material of the particles did not influence their entering. These results suggest that particles may penetrate the red blood cell membrane by a still unknown mechanism different from phagocytosis and endocytosis.