bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Exploratory User Study of Visual Causality Analysis
Authors: Yen Chi‐Hsien Eric , Parameswaran Aditya , Fu Wai‐Tat 
Published: July 2019

AbstractInteractive visualization tools are being used by an increasing number of members of the general public; however, little is known about how, and how well, people use visualizations to infer causality. Adapted from the mediation causal model, we designed an analytic framework to systematically evaluate human performance, strategies, and pitfalls in a visual causal reasoning task. We recruited 24 participants and asked them to identify the mediators in a fictitious dataset using bar charts and scatter plots within our visualization interface. The results showed that the accuracy of their responses as to whether a variable is a mediator significantly decreased when a confounding variable directly influenced the variable being analyzed. Further analysis demonstrated how individual visualization exploration strategies and interfaces might influence reasoning performance. We also identified common strategies and pitfalls in their causal reasoning processes. Design implications for how future visual analytics tools can be designed to better support causal inference are discussed.
A Visual Tool for the Analysis of Algorithms for Tomographic Fiber Reconstruction in Materials Science
Authors: Fröhler B. , Elberfeld T. , Möller T. , Hege H.C. , Weissenböck J. , De Beenhouwer J. , Sijbers J. , Kastner J. , Heinzl C. 
Published: July 2019

AbstractWe present visual analysis methods for the evaluation of tomographic fiber reconstruction algorithms by means of analysis, visual debugging and comparison of reconstructed fibers in materials science. The methods are integrated in a tool (FIAKER) that supports the entire workflow. It enables the analysis of various fiber reconstruction algorithms, of differently parameterized fiber reconstruction algorithms and of individual steps in iterative fiber reconstruction algorithms. Insight into the performance of fiber reconstruction algorithms is obtained by a list‐based ranking interface. A 3D view offers interactive visualization techniques to gain deeper insight, e.g., into the aggregated quality of the examined fiber reconstruction algorithms and parameterizations. The tool was designed in close collaboration with researchers who work with fiber‐reinforced polymers on a daily basis and develop algorithms for tomographic reconstruction and characterization of such materials. We evaluate the tool using synthetic datasets as well as tomograms of real materials. Five case studies certify the usefulness of the tool, showing that it significantly accelerates the analysis and provides valuable insights that make it possible to improve the fiber reconstruction algorithms. The main contribution of the paper is the well‐considered combination of methods and their seamless integration into a visual tool that supports the entire workflow. Further findings result from the analysis of (dis‐)similarity measures for fibers as well as from the discussion of design decisions. It is also shown that the generality of the analytical methods allows a wider range of applications, such as the application in pore space analysis.
Robust Extraction and Simplification of 2D Symmetric Tensor Field Topology
Authors: Jankowai Jochen , Wang Bei , Hotz Ingrid 
Published: July 2019

AbstractIn this work, we propose a controlled simplification strategy for degenerated points in symmetric 2D tensor fields that is based on the topological notion of robustness. Robustness measures the structural stability of the degenerate points with respect to variation in the underlying field. We consider an entire pipeline for generating a hierarchical set of degenerate points based on their robustness values. Such a pipeline includes the following steps: the stable extraction and classification of degenerate points using an edge labeling algorithm, the computation and assignment of robustness values to the degenerate points, and the construction of a simplification hierarchy. We also discuss the challenges that arise from the discretization and interpolation of real world data.
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization
Authors: Byška J. , Trautner T. , Marques S.M. , Damborský J. , Kozlíková B. , Waldner M. 
Published: July 2019

AbstractAnalyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. With increasing computational power, it is now possible to generate very long and complex simulations, which are cumbersome to explore using traditional 3D animations of protein movements. Guided by requirements derived from multiple focus groups with protein engineering experts, we designed and developed a novel interactive visual analysis approach for long and crowded MD simulations. In this approach, we link a dynamic 3D focus+context visualization with a 2D chart of time series data to guide the detection and navigation towards important spatio‐temporal events. The 3D visualization renders elements of interest in more detail and increases the temporal resolution dependent on the time series data or the spatial region of interest. In case studies with different MD simulation data sets and research questions, we found that the proposed visual analysis approach facilitates exploratory analysis to generate, confirm, or reject hypotheses about causalities. Finally, we derived design guidelines for interactive visual analysis of complex MD simulation data.
IGM‐Vis: Analyzing Intergalactic and Circumgalactic Medium Absorption Using Quasar Sightlines in a Cosmic Web Context
Authors: Burchett J.N. , Abramov D. , Otto J. , Artanegara C. , Prochaska J.X. , Forbes A.G. 
Published: July 2019

AbstractWe introduce IGM‐Vis, a novel astrophysics visualization and data analysis application for investigating galaxies and the gas that surrounds them in context with their larger scale environment, the Cosmic Web. Environment is an important factor in the evolution of galaxies from actively forming stars to quiescent states with little, if any, discernible star formation activity. The gaseous halos of galaxies (the circumgalactic medium, or CGM) play a critical role in their evolution, because the gas necessary to fuel star formation and any gas expelled from widely observed galactic winds must encounter this interface region between galaxies and the intergalactic medium (IGM). We present a taxonomy of tasks typically employed in IGM/CGM studies informed by a survey of astrophysicists at various career levels, and demonstrate how these tasks are facilitated via the use of our visualization software. Finally, we evaluate the effectiveness of IGM‐Vis through two in‐depth use cases that depict real‐world analysis sessions that use IGM/CGM data.
Evaluating image quality measures to assess the impact of lossy data compression applied to climate simulation data
Authors: Baker A. H. , Hammerling D. M. , Turton T. L. 
Published: July 2019

AbstractApplying lossy data compression to climate model output is an attractive means of reducing the enormous volumes of data generated by climate models. However, because lossy data compression does not exactly preserve the original data, its application to scientific data must be done judiciously. To this end, a collection of measures is being developed to evaluate various aspects of lossy compression quality on climate model output. Given the importance of data visualization to climate scientists interacting with model output, any suite of measures must include a means of assessing whether images generated from the compressed model data are noticeably different from images based on the original model data. Therefore, in this work we conduct a forced‐choice visual evaluation study with climate model data that surveyed more than one hundred participants with domain relevant expertise. In addition to the images created from unaltered climate model data, study images are generated from model data that is subjected to two different types of lossy compression approaches and multiple levels (amounts) of compression. Study participants indicate whether a visual difference can be seen, with respect to the reference image, due to lossy compression effects. We assess the relationship between the perceptual scores from the user study to a number of common (full reference) image quality assessment (IQA) measures, and use statistical models to suggest appropriate measures and thresholds for evaluating lossily compressed climate data. We find the structural similarity index (SSIM) to perform the best, and our findings indicate that the threshold required for climate model data is much higher than previous findings in the literature.
Designing Animated Transitions to Convey Aggregate Operations
Authors: Kim Younghoon , Correll Michael , Heer Jeffrey 
Published: July 2019

AbstractData can be aggregated in many ways before being visualized in charts, profoundly affecting what a chart conveys. Despite this importance, the type of aggregation is often communicated only via axis titles. In this paper, we investigate the use of animation to disambiguate different types of aggregation and communicate the meaning of aggregate operations. We present design rationales for animated transitions depicting aggregate operations and present the results of an experiment assessing the impact of these different transitions on identification tasks. We find that judiciously staged animated transitions can improve subjects' accuracy at identifying the aggregation performed, though sometimes with longer response times than with static transitions. Through an analysis of participants' rankings and qualitative responses, we find a consistent preference for animation over static transitions and highlight visual features subjects report relying on to make their judgments. We conclude by extending our animation designs to more complex charts of aggregated data such as box plots and bootstrapped confidence intervals.
Focus+Context Exploration of Hierarchical Embeddings
Authors: Höllt T. , Vilanova A. , Pezzotti N. , Lelieveldt B.P.F. , Hauser H. 
Published: July 2019

AbstractHierarchical embeddings, such as HSNE, address critical visual and computational scalability issues of traditional techniques for dimensionality reduction. The improved scalability comes at the cost of the need for increased user interaction for exploration. In this paper, we provide a solution for the interactive visual Focus+Context exploration of such embeddings. We explain how to integrate embedding parts from different levels of detail, corresponding to focus and context groups, in a joint visualization. We devise an according interaction model that relates typical semantic operations on a Focus+Context visualization with the according changes in the level‐of‐detail‐hierarchy of the embedding, including also a mode for comparative Focus+Context exploration and extend HSNE to incorporate the presented interaction model. In order to demonstrate the effectiveness of our approach, we present a use case based on the visual exploration of multi‐dimensional images.
InsideInsights: Integrating Data‐Driven Reporting in Collaborative Visual Analytics
Authors: Mathisen A. , Horak T. , Klokmose C. N. , Grønbæk K. , Elmqvist N. 
Published: July 2019

AbstractAnalyzing complex data is a non‐linear process that alternates between identifying discrete facts and developing overall assessments and conclusions. In addition, data analysis rarely occurs in solitude; multiple collaborators can be engaged in the same analysis, or intermediate results can be reported to stakeholders. However, current data‐driven communication tools are detached from the analysis process and promote linear stories that forego the hierarchical and branching nature of data analysis, which leads to either too much or too little detail in the final report. We propose a conceptual design for integrated data‐driven reporting that allows for iterative structuring of insights into hierarchies linked to analytic provenance and chosen analysis views. The hierarchies become dynamic and interactive reports where collaborators can review and modify the analysis at a desired level of detail. Our web‐based InsideInsights system provides interaction techniques to annotate states of analytic components, structure annotations, and link them to appropriate presentation views. We demonstrate the generality and usefulness of our system with two use cases and a qualitative expert review.
Investigating the Manual View Specification and Visualization by Demonstration Paradigms for Visualization Construction
Authors: Saket Bahador , Endert Alex 
Published: July 2019

AbstractInteractivity plays an important role in data visualization. Therefore, understanding how people create visualizations given different interaction paradigms provides empirical evidence to inform interaction design. We present a two‐phase study comparing people's visualization construction processes using two visualization tools: one implementing the manual view specification paradigm (Polestar) and another implementing visualization by demonstration (VisExemplar). Findings of our study indicate that the choice of interaction paradigm influences the visualization construction in terms of: 1) the overall effectiveness, 2) how participants phrase their goals, and 3) their perceived control and engagement. Based on our findings, we discuss trade‐offs and open challenges with these interaction paradigms.
Notes on Designer Entrepreneurs and “The Geppetto Effect”
Authors: Valencia Hernandez Jose Aldo , Pearce Alison 
Published: July 2019

The skills and talents of a design professional are not necessarily the skills and talents that will help them succeed with a startup business. Many “entrepreneur designers” could do with some help from professionals who can help them see the “big picture.”When designer entrepreneurs fall in love with their designs, the perfect can become the enemy of the good.
Future Directions: Design Meets Neuroscience
Authors: Flory Melanie , Ivanova Ninela 
Published: July 2019

Design thinking can find much material in the fields of psychology and neuroscience research, while neuroscience can benefit from design’s potential to influence and engage human beings. The authors of this article found that they had a lot to say to each other.A designer and a neuroscientist join forces and discover a whole new world.
Competitiveness of Czechoslovak exports under socialism and its impact on industries’ output growth after 1989
Authors: Coufalová Lucie , Mikula Štěpán , Žídek Libor 
Published: July 2019

AbstractThis paper addresses the performance of international trade during the centrally planned period in socialist Czechoslovakia and its consequences in the transition period. The goal of the paper is to determine whether the relative export competitiveness before 1989 positively influenced the performance of the enterprises in the transition period. To determine the reason for the low competitiveness of socialist enterprises, we use the oral history method, based on interviews with the then managers. We show that the level of competitiveness was influenced by multiple factors. Some of them were of a systemic nature, such as incentive structure, which did not encourage managers to pursue higher productivity, and others were related to day‐to‐day operations of the enterprises and a lack of Western technologies. Consequently, an econometric analysis is applied to determine whether there was any relationship between competitiveness in late socialism (ability to export to world markets) and production growth in the transition period. We expected that sectors that were able to export to Western markets during the centrally planned period were more successful after the fall of the regime. However, our findings do not support this hypothesis.
Genotype‐guided diagnostic reassessment after exome sequencing in neuromuscular disorders: experiences with a two‐step approach
Authors: Krenn M. , Tomschik M. , Rath J. , Cetin H. , Grisold A. , Zulehner G. , Milenkovic I. , Stogmann E. , Zimprich A. , Strom T. M. , Meitinger T. , Wagner M. , Zimprich F. 
Published: July 2019

Background and purposeNext‐generation sequencing has greatly improved the diagnostic success rates for genetic neuromuscular disorders (NMDs). Nevertheless, most patients still remain undiagnosed, and there is a need to maximize the diagnostic yield.MethodsA retrospective study was conducted on 72 patients with NMDs who underwent exome sequencing (ES), partly followed by genotype‐guided diagnostic reassessment and secondary investigations. The diagnostic yields that would have been achieved by appropriately chosen narrow and comprehensive gene panels were also analysed.ResultsThe initial diagnostic yield of ES was 30.6% (n = 22/72 patients). In an additional 15.3% of patients (n = 11/72) ES results were of unknown clinical significance. After genotype‐guided diagnostic reassessment and complementary investigations, the yield was increased to 37.5% (n = 27/72). Compared to ES, targeted gene panels (<25 kilobases) reached a diagnostic yield of 22.2% (n = 16/72), whereas comprehensive gene panels achieved 34.7% (n = 25/72).ConclusionExome sequencing allows the detection of pathogenic variants missed by (narrowly) targeted gene panel approaches. Diagnostic reassessment after genetic testing further enhances the diagnostic outcomes for NMDs.
A biophysical and structural study of two chitinases from Agave tequilana and their potential role as defense proteins
Authors: Sierra‐Gómez Yusvel , Rodríguez‐Hernández Annia , Cano‐Sánchez Patricia , Gómez‐Velasco Homero , Hernández‐Santoyo Alejandra , Siliqi Dritan , Rodríguez‐Romero Adela 
Published: July 2019

Plant chitinases are enzymes that have several functions, including providing protection against pathogens. Agave tequilana is an economically important plant that is poorly studied. Here, we identified a chitinase from short reads of the A. tequilana transcriptome (AtChi1). A second chitinase, differing by only six residues from the first, was isolated from total RNA of plants infected with Fusarium oxysporum (AtChi2). Both enzymes were overexpressed in Escherichia coli and analysis of their sequences indicated that they belong to the class I glycoside hydrolase family19, whose members exhibit two domains: a carbohydrate‐binding module and a catalytic domain, connected by a flexible linker. Activity assays and thermal shift experiments demonstrated that the recombinant Agave enzymes are highly thermostable acidic endochitinases with Tm values of 75 °C and 71 °C. Both exhibit a molecular mass close to 32 kDa, as determined by MALDI‐TOF, and experimental pIs of 3.7 and 3.9. Coupling small‐angle x‐ray scattering information with homology modeling and docking simulations allowed us to structurally characterize both chitinases, which notably show different interactions in the binding groove. Even when the six different amino acids are all exposed to solvent in the loops located near the linker and opposite to the binding site, they confer distinct kinetic parameters against colloidal chitin and similar affinity for (GlnNAc)6, as shown by isothermal titration calorimetry. Interestingly, binding is more enthalpy‐driven for AtChi2. Whereas the physiological role of these chitinases remains unknown, we demonstrate that they exhibit important antifungal activity against chitin‐rich fungi such as Aspergillus sp.DatabaseSAXS structural data are available in the SASBDB database with accession numbers SASDDE7 and SASDDA6.EnzymesChitinases (EC3.2.1.14).
Sailing together from different shores: labour markets and inequality on board merchant ships
Authors: ASPERS PATRIK , SANDBERG CARL 
Published: July 2019

AbstractIn this study, we analyse the consequences of the conditions of the labour‐market contracts for working on board merchant ships. More specifically, we examine how seafarers hired on different contracts work together. Seafarers’ conditions of work differ considerably: some, mainly workers in the West, have permanent contracts with a shipping company, are paid a relatively high monthly wage and can go ashore every second month, whereas others performing the same tasks may have to stay at sea for more than six months at a time, and work for less money on temporary contracts. Drawing on the economic sociology of markets and institutional theory, in this article we present the institutional conditions of globalized labour markets for seafarers and analyse unique data derived from observations and interviews on board merchant ships. We argue that the notion of market is a key explanatory factor for how the work is conducted on board. Theoretically, our elaboration on markets allows us to conceptualize and address global and transnational markets.
Modeling a Large‐Scale Historic Aquifer Test: Insight into the Hydrogeology of a Regional Fault Zone
Authors: Hadley Daniel R. , Abrams Daniel B. , Roadcap George S. 
Published: July 2019

AbstractFaults can act as flow barriers or conduits to groundwater flow by introducing heterogeneity in permeability. We examine the hydrogeology of the Sandwich Fault Zone, a 137 km long zone of high‐angle faults in northern Illinois, using a large‐scale historic aquifer test. The fault zone is poorly understood at depth due to the majority of the faults being buried by glacial deposits and its near‐vertical orientation which limits geologic sampling across faults. The aquifer test—perhaps one of the largest in terms of overall withdrawal in North American history—was conducted in 1942 at a facility adjacent to the fault zone. More than 34,000 m3/day was pumped for 37 days from nine multiaquifer wells open to the stratified Cambrian‐Ordovician sandstone aquifer system. We modeled the aquifer test using a transient MODFLOW‐USG model and simulated pumping wells with the CLN package. We tested numerous fault core/damage zone conceptualizations and calibrated to drawdown values recorded at production and observation wells. Our analysis indicates that the fault zone is a low‐permeability feature that inhibits lateral movement of groundwater and that there is at least an order of magnitude decrease in horizontal hydraulic conductivity in the fault core compared to the undeformed sandstone. Large head declines have occurred north of the fault zone (over 300 m since predevelopment conditions) and modifying fault zone parameters significantly affects calibration to regional drawdown on a decadal scale. The flow‐barrier behavior of the fault zone has important implications for future groundwater availability in this highly stressed region.