bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel Marching Blocks: A Practical Isosurfacing Algorithm for Large Data on Many‐Core Architectures
Authors: Liu Baoquan , Clapworthy Gordon J. , Dong Feng , Wu Enhua 
Published: July 2016

AbstractInteractive isosurface visualisation has been made possible by mapping algorithms to GPU architectures. However, current state‐of‐the‐art isosurfacing algorithms usually consume large amounts of GPU memory owing to the additional acceleration structures they require. As a result, the continued limitations on available GPU memory mean that they are unable to deal with the larger datasets that are now increasingly becoming prevalent.This paper proposes a new parallel isosurface‐extraction algorithm that exploits the blocked organisation of the parallel threads found in modern many‐core platforms to achieve fast isosurface extraction and reduce the associated memory requirements. This is achieved by optimising thread co‐operation within thread‐blocks and reducing redundant computation; ultimately, an indexed triangular mesh can be produced.Experiments have shown that the proposed algorithm is much faster (up to 10×) than state‐of‐the‐art GPU algorithms and has a much smaller memory footprint, enabling it to handle much larger datasets (up to 64×) on the same GPU.
Faceted Views of Varying Emphasis (FaVVEs): a framework for visualising multi‐perspective small multiples
Authors: Beecham R. , Rooney C. , Meier S. , Dykes J. , Slingsby A. , Turkay C. , Wood J. , Wong B.L. W. 
Published: July 2016

AbstractMany datasets have multiple perspectives – for example space, time and description – and often analysts are required to study these multiple perspectives concurrently. This concurrent analysis becomes difficult when data are grouped and split into small multiples for comparison. A design challenge is thus to provide representations that enable multiple perspectives, split into small multiples, to be viewed simultaneously in ways that neither clutter nor overload. We present a design framework that allows us to do this. We claim that multi‐perspective comparison across small multiples may be possible by superimposing perspectives on one another rather than juxtaposing those perspectives side‐by‐side. This approach defies conventional wisdom and likely results in visual and informational clutter. For this reason we propose designs at three levels of abstraction for each perspective. By flexibly varying the abstraction level, certain perspectives can be brought into, or out of, focus. We evaluate our framework through laboratory‐style user tests. We find that superimposing, rather than juxtaposing, perspective views has little effect on performance of a low‐level comparison task. We reflect on the user study and its design to further identify analysis situations for which our framework may be desirable. Although the user study findings were insufficiently discriminating, we believe our framework opens up a new design space for multi‐perspective visual analysis.
Visual Debugging Techniques for Reactive Data Visualization
Authors: Hoffswell Jane , Satyanarayan Arvind , Heer Jeffrey 
Published: July 2016

AbstractInteraction is critical to effective visualization, but can be difficult to author and debug due to dependencies among input events, program state, and visual output. Recent advances leverage reactive semantics to support declarative design and avoid the “spaghetti code” of imperative event handlers. While reactive programming improves many aspects of development, textual specifications still fail to convey the complex runtime dynamics. In response, we contribute a set of visual debugging techniques to reveal the runtime behavior of reactive visualizations. A timeline view records input events and dynamic variable updates, allowing designers to replay and inspect the propagation of values step‐by‐step. On‐demand annotations overlay the output visualization to expose relevant state and scale mappings in‐situ. Dynamic tables visualize how backing datasets change over time. To evaluate the effectiveness of these techniques, we study how first‐time Vega users debug interactions in faulty, unfamiliar specifications; with no prior knowledge, participants were able to accurately trace errors through the specification.
BubbleNet: A Cyber Security Dashboard for Visualizing Patterns
Authors: McKenna S. , Staheli D. , Fulcher C. , Meyer M. 
Published: July 2016

AbstractThe field of cyber security is faced with ever‐expanding amounts of data and a constant barrage of cyber attacks. Within this space, we have designed BubbleNet as a cyber security dashboard to help network analysts identify and summarize patterns within the data. This design study faced a range of interesting constraints from limited time with various expert users and working with users beyond the network analyst, such as network managers. To overcome these constraints, the design study employed a user‐centered design process and a variety of methods to incorporate user feedback throughout the design of BubbleNet. This approach resulted in a successfully evaluated dashboard with users and further deployments of these ideas in both research and operational environments. By explaining these methods and the process, it can benefit future visualization designers to help overcome similar challenges in cyber security or alternative domains.
Semi‐automatic Vortex Flow Classification in 4D PC‐MRI Data of the Aorta
Authors: Meuschke M. , Köhler B. , Preim U. , Preim B. , Lawonn K. 
Published: July 2016

AbstractWe present an Aortic Vortex Classification (AVOCLA) that allows to classify vortices in the human aorta semi‐automatically. Current medical studies assume a strong relation between cardiovascular diseases and blood flow patterns such as vortices. Such vortices are extracted and manually classified according to specific, unstandardized properties. We employ an agglomerative hierarchical clustering to group vortex‐representing path lines as basis for the subsequent classification. Classes are based on the vortex' size, orientation and shape, its temporal occurrence relative to the cardiac cycle as well as its spatial position relative to the vessel course. The classification results are presented by a 2D and 3D visualization technique. To confirm the usefulness of both approaches, we report on the results of a user study. Moreover, AVOCLA was applied to 15 datasets of healthy volunteers and patients with different cardiovascular diseases. The results of the semi‐automatic classification were qualitatively compared to a manually generated ground truth of two domain experts considering the vortex number and five specific properties.
Critical Points of Gaussian‐Distributed Scalar Fields on Simplicial Grids
Authors: Liebmann T. , Scheuermann G. 
Published: July 2016

AbstractSimulations and measurements often result in scalar fields with uncertainty due to errors or output sensitivity estimates. Methods for analyzing topological features of such fields usually are not capable of handling all aspects of the data. They either are not deterministic due to using Monte Carlo approaches, approximate the data with confidence intervals, or miss out on incorporating important properties, such as correlation. In this paper, we focus on the analysis of critical points of Gaussian‐distributed scalar fields. We introduce methods to deterministically extract critical points, approximate their probability with high precision, and even capture relations between them resulting in an abstract graph representation. Unlike many other methods, we incorporate all information contained in the data including global correlation. Our work therefore is a first step towards a reliable and complete description of topological features of Gaussian‐distributed scalar fields.
Location‐dependent generalization of road networks based on equivalent destinations
Authors: van Dijk Thomas C. , Haunert Jan‐Henrik , Oehrlein Johannes 
Published: July 2016

AbstractSuppose a user located at a certain vertex in a road network wants to plan a route using a wayfinding map. The user's exact destination may be irrelevant for planning most of the route, because many destinations will be equivalent in the sense that they allow the user to choose almost the same paths. We propose a method to find such groups of destinations automatically and to contract the resulting clusters in a detailed map to achieve a simplified visualization. We model the problem as a clustering problem in rooted, edge‐weighted trees. Two vertices are allowed to be in the same cluster if and only if they share at least a given fraction of their path to the root. We analyze some properties of these clusterings and give a linear‐time algorithm to compute the minimum‐cardinality clustering. This algorithm may have various other applications in network visualization and graph drawing, but in this paper we apply it specifically to focus‐and‐context map generalization. When contracting shortest‐path trees in a geographic network, the computed clustering additionally provides a constant‐factor bound on the detour that results from routing using the generalized network instead of the full network. This is a desirable property for wayfinding maps.
AVOCADO: Visualization of Workflow–Derived Data Provenance for Reproducible Biomedical Research
Authors: Stitz H. , Luger S. , Streit M. , Gehlenborg N. 
Published: July 2016

AbstractA major challenge in data‐driven biomedical research lies in the collection and representation of data provenance information to ensure that findings are reproducibile. In order to communicate and reproduce multi‐step analysis workflows executed on datasets that contain data for dozens or hundreds of samples, it is crucial to be able to visualize the provenance graph at different levels of aggregation. Most existing approaches are based on node‐link diagrams, which do not scale to the complexity of typical data provenance graphs. In our proposed approach, we reduce the complexity of the graph using hierarchical and motif‐based aggregation. Based on user action and graph attributes, a modular degree‐of‐interest (DoI) function is applied to expand parts of the graph that are relevant to the user. This interest‐driven adaptive approach to provenance visualization allows users to review and communicate complex multi‐step analyses, which can be based on hundreds of files that are processed by numerous workflows. We have integrated our approach into an analysis platform that captures extensive data provenance information, and demonstrate its effectiveness by means of a biomedical usage scenario.
Visual Analysis of Biomolecular Cavities: State of the Art
Authors: Krone M. , Kozlíková B. , Lindow N. , Baaden M. , Baum D. , Parulek J. , Hege H.‐C. , Viola I. 
Published: July 2016

AbstractIn this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid‐based, Voronoi‐based, surface‐based, and probe‐based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non‐spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.
State‐of‐the‐Art Report in Web‐based Visualization
Authors: Mwalongo F. , Krone M. , Reina G. , Ertl T. 
Published: July 2016

AbstractIn this report, we review the current state of the art of web‐based visualization applications. Recently, an increasing number of web‐based visualization applications have emerged. This is due to the fact that new technologies offered by modern browsers greatly increased the capabilities for visualizations on the web. We first review these technical aspects that are enabling this development. This includes not only improvements for local rendering like WebGL and HTML5, but also infrastructures like grid or cloud computing platforms. Another important factor is the transfer of data between the server and the client. Therefore, we also discuss advances in this field, for example methods to reduce bandwidth requirements like compression and other optimizations such as progressive rendering and streaming. After establishing these technical foundations, we review existing web‐based visualization applications and prototypes from various application domains. Furthermore, we propose a classification of these web‐based applications based on the technologies and algorithms they employ. Finally, we also discuss promising application areas that would benefit from web‐based visualization and assess their feasibility based on the existing approaches.
State of the Art in Transfer Functions for Direct Volume Rendering
Authors: Ljung Patric , Krüger Jens , Groller Eduard , Hadwiger Markus , Hansen Charles D. , Ynnerman Anders 
Published: July 2016

AbstractA central topic in scientific visualization is the transfer function (TF) for volume rendering. The TF serves a fundamental role in translating scalar and multivariate data into color and opacity to express and reveal the relevant features present in the data studied. Beyond this core functionality, TFs also serve as a tool for encoding and utilizing domain knowledge and as an expression for visual design of material appearances. TFs also enable interactive volumetric exploration of complex data. The purpose of this state‐of‐the‐art report (STAR) is to provide an overview of research into the various aspects of TFs, which lead to interpretation of the underlying data through the use of meaningful visual representations. The STAR classifies TF research into the following aspects: dimensionality, derived attributes, aggregated attributes, rendering aspects, automation, and user interfaces. The STAR concludes with some interesting research challenges that form the basis of an agenda for the development of next generation TF tools and methodologies.
Formalizing Emphasis in Information Visualization
Authors: Hall K. Wm. , Perin C. , Kusalik P. G. , Gutwin C. , Carpendale S. 
Published: July 2016

AbstractWe provide afresh look at the use and prevalence of emphasis effects in Infovis. Through a survey of existing emphasis frameworks, we extract a set‐based approach that uses visual prominence to link visually and algorithmically diverse emphasis effects. Visual prominence provides a basis for describing, comparing and generating emphasis effects when combined with a set of general features of emphasis effects. Therefore, we use visual prominence and these general features to construct a new mathematical Framework for Information Visualization Emphasis, FIVE. The concepts we introduce to describe FIVE unite the emphasis literature and point to several new research directions for emphasis in information visualization.
Sacral nerve stimulation lead implantation in partial sacral agenesis using intra‐operative computerized tomography
Authors: Castillo J. , Cristóbal L. , Alonso J. , Martín R. , Suárez D. , Martínez M. A. , Cagigas C. , Gómez‐Ruiz M. , Gómez‐Fleitas M. , Vázquez‐Barquero A. 
Published: July 2016

AbstractAimSacral nerve stimulation (SNS) lead implantation is a straightforward procedure for individuals with intact spinal vertebrae. When sacral anomalies are present, however, the anatomical and radiological reference points used for the accurate placement of the electrode may be absent or difficult to identify.MethodWe describe an innovative surgical procedure of percutaneous nerve evaluation for SNS in a patient with faecal incontinence secondary to a congenital imperforate anus and partial sacral agenesis using a surgical imaging platform (O‐arm system) under neurophysiological control.ResultsUsing intra‐operative CT and neuronavigation, the insertion point at the skin was identified. The lead was introduced into the right‐sided S3 foramen and placed at the correct depth. An appropriate motor response was obtained after stimulation and neurophysiological control confirmed that the right S3 root was being stimulated.ConclusionOur experience showed that O‐arm guided navigation can be used to overcome the difficulty of SNS lead placement in patients with partial sacral agenesis who have faecal incontinence.
Consistent Extinction Risk Assessment under the U.S. Endangered Species Act
Authors: Boyd Charlotte , DeMaster Douglas P. , Waples Robin S. , Ward Eric J. , Taylor Barbara L. 
Published: July 2016

AbstractIdentifying species at risk of extinction is essential for effective conservation priority‐setting in the face of accelerating biodiversity loss. However, the levels of risk that lead to endangered or threatened listing decisions under the United States Endangered Species Act (ESA) are not well defined. We used a Bayesian population modeling approach to estimate levels of risk consistently for 14 marine species previously assessed under the ESA. For each species, we assessed the risks of declining below various abundance thresholds over various time horizons. We found that high risks of declining below 250 mature individuals within five generations matched well with ESA endangered status, while number of populations was useful for distinguishing between threatened and “not warranted” species. The risk assessment framework developed here could enable more consistent, predictable, and transparent ESA status assessments in the future.
Significant and Timely Ivory Trade Restrictions in Both China and the United States are Critical to Save Elephants
Authors: Yu Yang , Wetzler Andrew , Yang Xuan , Tang Ruchun , Zhang Li 
Published: July 2016

AbstractThe United States and China have committed to enact “nearly complete bans” on the import and export of elephant ivory, including putting in place significant and timely restrictions on the import of ivory as hunting trophies, and taking swift steps to halt their domestic ivory trade. Unlike the United States, China has to move forward on its commitment to further restrict its domestic commercial trade. This is primarily due to China's existing certificated ivory manufacturers and retailers who own huge legal ivory stockpiles. We propose that the Chinese government use its eco‐compensation funds to purchase back all legal ivory from the market. This “decommodification” could help save the elephant population worldwide. Alternatively, China could enact a domestic ban with a short phase‐in period (a similar approach has been adopted by several U.S. States) to allow legal ivory merchants to sell their stockpiles. A hybrid of these two approaches could also be considered.
Spiritual well‐being and coping in scleroderma, lupus erythematosus, and melanoma
Authors: Pilch Michaela , Scharf Sabina Nadine , Lukanz Martin , Wutte Nora Johanna , Fink‐Puches Regina , Glawischnig‐­Goschnik Monika , Unterrainer Human‐Friedrich , Aberer Elisabeth 
Published: July 2016

SummaryBackground and objectivesReligious/spiritual (R‐S) well‐being is associated with greater vitality and lower depression scores. In this study, we investigated strategies for coping with disease and the role of religiosity/spirituality with respect to improving subjective well‐being.Patients and methodsOne hundred and forty‐nine patients (107 women), 44 of whom with systemic sclerosis (SSc), 48 with lupus erythematosus (LE), and 57 with stage I or II malignant melanoma (MM) were surveyed using a self‐designed questionnaire, which addressed subjective well‐being and disease‐related circumstances, as well as the Multidimensional Inventory for Religious/Spiritual Well‐Being (MI‐RSWB).ResultsAt the time of diagnosis, disease burden is greater in LE patients than in patients with SSc and MM. Only after several years are SSc and LE patients able to accept their disease. Compared with healthy individuals, the overall score of R‐S well‐being is significantly lower in LE patients. In LE, photosensitivity and joint pain are inversely correlated with the ability to forgive. SSc patients with facial lesions and pulmonary involvement show greater religiosity. MM patients display significantly higher values for transcendental hope.ConclusionTalks about the disease and psychological support are the most important needs of patients with SSc, LE, and MM. At present, programs aimed at improving R‐S coping skills do not seem to play a significant role, but could be an important resource that should be addressed in the future.
Checkpoint‐Inhibitoren in der Immuntherapie: Ein Meilenstein in der Behandlung des malignen Melanoms
Authors: Wilden Sophia M. , Lang Berenice M. , Mohr Peter , Grabbe Stephan 
Published: July 2016

ZusammenfassungSeit Jahrzehnten ist bekannt, dass Tumoren vom Immunsystem erkannt und zerstört werden können. Diese, vor allem in Tierversuchen gewonnene Erkenntnis konnte jedoch in der Vergangenheit nicht zum Nutzen unserer Patienten umgesetzt werden, da immunonkologische Therapieansätze in den letzten Jahrzehnten in der Anwendung beim Menschen stets versagt haben. Daher hat, mit Ausnahme der adjuvanten Interferontherapie, keines dieser Verfahren den Einzug in die klinische Versorgung gefunden. Langzeitüberleben unter guter Lebensqualität war dabei sehr wenigen Patienten vorbehalten. Mit den neuen immunologischen Therapieansätzen wird jedoch sowohl das Langzeitüberleben als auch die Lebensqualität onkologischer Patienten neu definiert. Auf die neuen „Immun‐Checkpoint‐Inhibitoren“ spricht erstmals ein relevanter Teil der behandelten Patienten an und diese zeigen in der Regel langandauernde Remissionen bis hin zur Heilung. Schon jetzt ist klar, dass die Immuntherapie in Zukunft eine der wesentlichen Therapiesäulen bei der Behandlung des metastasierten Melanoms und auch vieler anderer fortgeschrittener Tumoren bilden wird. In dieser Übersicht werden die wichtigsten neuen Therapiemodalitäten besprochen und sowohl deren Wirkprinzip als auch klinische Daten zum Therapieansprechen und zu erwartenden Nebenwirkungen der Therapie referiert.