The Topology ToolKit

This system paper presents the Topology ToolKit (TTK), a software platform designed for topological data analysis in scientific visualization. TTK provides a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due to a tight integration with ParaView. It is also easily accessible to developers through a variety of bindings (Python, VTK/C++) for fast prototyping or through direct, dependence-free, C++, to ease integration into pre-existing complex systems. While developing TTK, we faced several algorithmic and software engineering challenges, which we document in this paper. In particular, we present an algorithm for the construction of a discrete gradient that complies to the critical points extracted in the piecewise-linear setting. This algorithm guarantees a combinatorial consistency across the topological abstractions supported by TTK, and importantly, a unified implementation of topological data simplification for multi-scale exploration and analysis. We also present a cached triangulation data structure, that supports time efficient and generic traversals, which self-adjusts its memory usage on demand for input simplicial meshes and which implicitly emulates a triangulation for regular grids with no memory overhead. Finally, we describe an original software architecture, which guarantees memory efficient and direct accesses to TTK features, while still allowing for researchers powerful and easy bindings and extensions. TTK is open source (BSD license) and its code, online documentation and video tutorials are available on TTK's website

The Human Chromogranin A Gene: Chromosome Assignment and RFLP Analysis.

Chromogranin A/secretory protein I (CgA) is a glycoprotein that is stored and released along with peptide hormones and neurotransmitters from several tissues, although its exact function is not known. A cDNA (gene symbol CHGA) clone was used as a probe in Southern blot analyses of human-rodent somatic cell hybrid DNAs. Discordancy analysis allowed confirmation of the assignment of the gene to chromosome 14. These results were extended using in situ chromosome hybridization, and a signal was found at 14q32. BglII digestion of genomic DNA from 28 unrelated Caucasian individuals probed with CHGA detected a two-allele RFLP with allelic frequencies of .34 and .66

Chronicling Catastrophe and Constructing Urban Destruction: Asai Ryōi's Musashi Abumi and Kanameishi

This thesis examines two works by Asai Ryōi (?-1691) 浅井了意 that depict urban disasters. The first is Musashi abumi むさしあぶみ (1661), which deals with a fire that ravaged Edo in 1657; the second is Kanameishi かなめいし (ca. 1662), which is about an earthquake that occurred in Kyoto in 1662. Despite being written by the same person, these works use very different strategies in their respective representations of urban catastrophe. In engaging these texts, I focus on the various contexts in which Ryōi wrote them—contexts related to place, literary tradition, and the catastrophic events themselves—to illuminate why these works are so different. In emphasizing these texts’ historically-grounded diversity, I argue that we can broaden our perspective on what constitutes “disaster writing” in a way that moves away from conceptions of such writing as “speaking the unspeakable.

Transits and Occultations of an Earth-Sized Planet in an 8.5-Hour Orbit

We report the discovery of an Earth-sized planet ($1.16\pm 0.19 R_\oplus$) in an 8.5-hour orbit around a late G-type star (KIC 8435766, Kepler-78). The object was identified in a search for short-period planets in the {\it Kepler} database and confirmed to be a transiting planet (as opposed to an eclipsing stellar system) through the absence of ellipsoidal light variations or substantial radial-velocity variations. The unusually short orbital period and the relative brightness of the host star ($m_{\rm Kep}$ = 11.5) enable robust detections of the changing illumination of the visible hemisphere of the planet, as well as the occultations of the planet by the star. We interpret these signals as representing a combination of reflected and reprocessed light, with the highest planet dayside temperature in the range of 2300 K to 3100 K. Follow-up spectroscopy combined with finer sampling photometric observations will further pin down the system parameters and may even yield the mass of the planet.Comment: Accepted for publication, ApJ, 10 pages and 6 figure

Theories of the deep: combining salience and network analyses to produce mental model visualizations of a coastal British Columbia food web

Arriving at shared mental models among multiple stakeholder groups can be crucial for successful management of contested social-ecological systems (SES). Academia can help by first eliciting stakeholders’ initial, often tacit, beliefs about a SES, and representing them in useful ways. We demonstrate a new recombination of techniques for this purpose, focusing specifically on tacit beliefs about food webs. Our approach combines freelisting and sorting techniques, salience analysis, and ultimately network analysis, to produce accessible visualizations of aggregate mental models that can then be used to facilitate discussion or generate further hypotheses about cognitive drivers of conflict. The case study we draw upon to demonstrate this technique is Clayoquot Sound UNESCO Biosphere Reserve, on the west coast of British Columbia, Canada. There, an immanent upsurge in the sea otter (Enhydra lutris) population, which competes with humans for shellfish, has produced tension among government managers, and both First Nations and non-First Nations residents. Our approach helps explain this tension by visually highlighting which trophic relationships appear most cognitively salient among the lay public. We also include speculative representations of models held by managers, and pairs of contrasting demographic subgroups, to further demonstrate potential uses of the method

Determination of biomembrane bending moduli in fully atomistic simulations.

The bilayer bending modulus (Kc) is one of the most important physical constants characterizing lipid membranes, but precisely measuring it is a challenge, both experimentally and computationally. Experimental measurements on chemically identical bilayers often differ depending upon the techniques employed, and robust simulation results have previously been limited to coarse-grained models (at varying levels of resolution). This Communication demonstrates the extraction of Kc from fully atomistic molecular dynamics simulations for three different single-component lipid bilayers (DPPC, DOPC, and DOPE). The results agree quantitatively with experiments that measure thermal shape fluctuations in giant unilamellar vesicles. Lipid tilt, twist, and compression moduli are also reported

Determination of Mercury in an Assortment of Dietary Supplements Using an Inexpensive Combustion Atomic Absorption Spectrometry Technique

The concentrations of mercury in forty, commercially available dietary supplements, were determined using a new, inexpensive analysis technique. The method involves thermal decomposition, amalgamation, and detection of mercury by atomic absorption spectrometry with an analysis time of approximately six minutes per sample. The primary cost savings from this approach is that labor-intensive sample digestion is not required prior to analysis, further automating the analytical procedure. As a result, manufacturers and regulatory agencies concerned with monitoring lot-to-lot product quality may find this approach an attractive alternative to the more classical acid-decomposition, cold vapor atomic absorption methodology. Dietary supplement samples analyzed included astragalus, calcium, chromium picolinate, echinacea, ephedra, fish oil, ginger, ginkgo biloba, ginseng, goldenseal, guggul, senna, St John's wort, and yohimbe products. Quality control samples analyzed with the dietary supplements indicated a high level of method accuracy and precision. Ten replicate preparations of a standard reference material (NIST 1573a, tomato leaves) were analyzed, and the average mercury recovery was 109% (2.0% RSD). The method quantitation limit was 0.3 ng, which corresponded to 1.5 ng/g sample. The highest found mercury concentration (123 ng/g) was measured in a concentrated salmon oil sample. When taken as directed by an adult, this product would result in an approximate mercury ingestion of 7 μg per week

PROCESSING OF HYDROXYLAPATITE COATINGS ON TITANIUM ALLOY BONE PROSTHESES

Processing of hydroxylapatite Sol-gel films on titanium alloy bone prostheses. A method utilizing non-line-of-Sight ion beam implantation and/or rapid thermal processing to provide improved bonding of layers of hydroxylapatite to titanium alloy Substrates while encouraging bone ingrowth into the hydroxylapatite layers located away from the substrate, is described for the fabrication of prostheses. The first layer of hydroxylapatite is mixed into the Substrate by the ions or rapidly thermally annealed, while Subsequent layers are heat treated or densified using ion implantation to form layers of decreasing density and larger crystallization, with the outermost layers being Suitable for bone ingrowth

Etidronate prevents, but does not reverse, ectopic mineralization in a mouse model of pseudoxanthoma elasticum (

Pseudoxanthoma elasticum (PXE) and generalized arterial calcification of infancy (GACI) are heritable disorders manifesting with ectopic tissue mineralization. Most cases of PXE and some cases of GACI are caused by mutations in the ABCC6 gene, resulting in reduced plasma pyrophosphate (PPi) levels. There is no effective treatment for these disorders. It has been suggested that administration of bisphosphonates, stable and non-hydrolyzable PPi analogs, could counteract ectopic mineralization in these disorders. In this study we tested the potential efficacy of etidronate, a first generation bisphosphonate, on ectopic mineralization in the muzzle skin of Abcc6-/- mice, a model of PXE. The Abcc6-/- mice received subcutaneous injections of etidronate, 0.283 and 3.40 mg/kg per injection (0.01× and 0.12×), twice a week, in both prevention and reversal studies. Ectopic mineralization in the dermal sheath of vibrissae in muzzle skin was determined by histopathologic analysis and by direct chemical assay for calcium content. Subcutaneous injection of etidronate prevented ectopic mineralization but did not reverse existing mineralization. The effect of etidronate was accompanied by alterations in the trabecular bone microarchitecture, determined by micro-computed tomography. The results suggest that etidronate may offer a potential treatment modality for PXE and GACI caused by ABCC6 mutations. Etidronate therapy should be initiated in PXE patients as soon as the diagnosis is made, with careful monitoring of potential side effects

Simultaneous Exoplanet Characterization and deep wide-field imaging with a diffractive pupil telescope

High-precision astrometry can identify exoplanets and measure their orbits and masses, while coronagraphic imaging enables detailed characterization of their physical properties and atmospheric compositions through spectroscopy. In a previous paper, we showed that a diffractive pupil telescope (DPT) in space can enable sub-microarcsecond accuracy astrometric measurements from wide-field images by creating faint but sharp diffraction spikes around the bright target star. The DPT allows simultaneous astrometric measurement and coronagraphic imaging, and we discuss and quantify in this paper the scientific benefits of this combination for exoplanet science investigations: identification of exoplanets with increased sensitivity and robustness, and ability to measure planetary masses to high accuracy. We show how using both measurements to identify planets and measure their masses offers greater sensitivity and provides more reliable measurements than possible with separate missions, and therefore results in a large gain in mission efficiency. The combined measurements reliably identify potentially habitable planets in multiple systems with a few observations, while astrometry or imaging alone would require many measurements over a long time baseline. In addition, the combined measurement allows direct determination of stellar masses to percent-level accuracy, using planets as test particles. We also show that the DPT maintains the full sensitivity of the telescope for deep wide-field imaging, and is therefore compatible with simultaneous scientific observations unrelated to exoplanets. We conclude that astrometry, coronagraphy, and deep wide-field imaging can be performed simultaneously on a single telescope without significant negative impact on the performance of any of the three techniques.Comment: 15 pages, 6 figures. This second paper, following the paper describing the diffractive pupil telescope (DPT) astrometric technique, shows how simultaneous astrometry and coronagraphy observations, enabled by the DPT concept, constrain the orbital parameters and mass of exoplanet