The impact of hyperlinks, skim reading and perceived importance when reading on the Web.

It has previously been shown that readers spend a great deal of time skim reading on the Web and that this type of reading can affect comprehension of text. Across two experiments, we examine how hyperlinks influence perceived importance of sentences and how perceived importance in turn affects reading behaviour. In Experiment 1, participants rated the importance of sentences across passages of Wikipedia text. In Experiment 2, a different set of participants read these passages while their eye movements were tracked, with the task being either reading for comprehension or skim reading. Reading times of sentences were analysed in relation to the type of task and the importance ratings from Experiment 1. Results from Experiment 1 show readers rated sentences without hyperlinks as being of less importance than sentences that did feature hyperlinks, and this effect is larger when sentences are lower on the page. It was also found that short sentences with more links were rated as more important, but only when they were presented at the top of the page. Long sentences with more links were rated as more important regardless of their position on the page. In Experiment 2, higher importance scores resulted in longer sentence reading times, measured as fixation durations. When skim reading, however, importance ratings had a lesser impact on online reading behaviour than when reading for comprehension. We suggest readers are less able to establish the importance of a sentence when skim reading, even though importance could have been assessed by information that would be fairly easy to extract (i.e. presence of hyperlinks, length of sentences, and position on the screen).

Graphical integrity issues in open access publications: Detection and patterns of proportional ink violations.

Academic graphs are essential for communicating complex scientific ideas and results. To ensure that these graphs truthfully reflect underlying data and relationships, visualization researchers have proposed several principles to guide the graph creation process. However, the extent of violations of these principles in academic publications is unknown. In this work, we develop a deep learning-based method to accurately measure violations of the proportional ink principle (AUC = 0.917), which states that the size of shaded areas in graphs should be consistent with their corresponding quantities. We apply our method to analyze a large sample of bar charts contained in 300K figures from open access publications. Our results estimate that 5% of bar charts contain proportional ink violations. Further analysis reveals that these graphical integrity issues are significantly more prevalent in some research fields, such as psychology and computer science, and some regions of the globe. Additionally, we find no temporal and seniority trends in violations. Finally, apart from openly releasing our large annotated dataset and method, we discuss how computational research integrity could be part of peer-review and the publication processes.

[Shapes or icons from the dietary guidelines. A reality going beyond healthy food]. / Grafismos o iconos provenientes de las guías alimentarias. Una realidad que va más allá de la alimentación saludable.

INTRODUCTION: Background: icons or shapes represent the development and approval of dietary guidelines including recommendations of food consumption and nutrient intakes according to the behavioral models of countries worldwide. The Food and Agriculture Organization (FAO) collected and recognized them. Methods: food-based dietary guidelines from 94 countries included in the FAO website. Websites of the different Spanish scientific societies that have elaborated and developed them, including the Mediterranean Diet Foundation. Results: in all, 94 countries are collected in the FAO food guidelines website, with predominant models of 33 diet plates and 51 food pyramids, emerging 11 as new graphics systems, that reflect, in addition to food: 52, physical activity; 63, water or hydration; 20, social and emotional values; and 13, reduction or elimination of alcoholic beverages. Conclusions: the models with icons or shapes so far are consistent with the modes of distribution of food at meals and adapting to new criteria that include behavioral guidelines. New designs are incorporated that include food safety guidelines in generic graphic structures that do not represent any of the classic models: food plates or food pyramids.

INTRODUCCIÓN: Fundamentos: el desarrollo y la aprobación de guías alimentarias, con recomendación de consumo de alimentos y de ingestas de nutrientes según los distintos modelos comportamentales de los países a nivel mundial, culmina con la creación de iconos o grafismos que las representan. Estos, además, son recogidos y reconocidos por la Organización para la Alimentación y la Agricultura (FAO). Métodos: guías alimentarias de 94 países incluidas en la web de la FAO y de las diferentes sociedades científicas españolas que las tienen elaboradas y desarrolladas, así como la de la Fundación Dieta Mediterránea. Resultados: en la web de la FAO se recogen 94 países con modelos predominantes de 33 platos y 51 pirámides, surgiendo 11 casos de sistema nuevo que plasman, además de alimentos: 52, actividad física; 63, agua o hidratación; 20, aspectos sociales y emocionales, y 13, reducción o eliminación de bebidas alcohólicas. Conclusiones: los modelos de iconos o grafismos hasta ahora son parejos con los modos de distribución de alimentos en las comidas, adaptándose a los nuevos criterios que incluyen pautas comportamentales. Se incorporan nuevos diseños que incluyen pautas de seguridad alimentaria en estructuras gráficas genéricas que no representan ninguno de los modelos clásicos (platos o pirámides alimentarios).

Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation.

This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to design and analysis of a range of DNA/RNA nanostructures.

Guidelines for Reporting of Figures and Tables for Clinical Research in Urology.

In an effort to improve the presentation of and information within tables and figures in clinical urology research, we propose a set of appropriate guidelines. We introduce six principles: (1) include graphs only if they improve the reader's ability to understand the study findings; (2) think through how a graph might best convey information, do not just select a graph from preselected options on statistical software; (3) do not use graphs to replace reporting key numbers in the text of a paper; (4) graphs should give an immediate visual impression of the data; (5) make it beautiful; and (6) make the labels and legend clear and complete. We present a list of quick "dos and don'ts" for both tables and figures. Investigators should feel free to break any of the guidelines if it would result in a beautiful figure or a clear table that communicates data effectively. That said, we believe that the quality of tables and figures in the medical literature would improve if these guidelines were to be followed. Patient summary: A set of guidelines were developed for presenting figures and tables in urology research. The guidelines were developed by a broad group of statistical experts with special interest in urology.

C1 triangular Coons surface construction and image interpolation based on new Side-Side and Side-Vertex interpolation operators.

In this paper, a new class of rational quadratic/linear trigonometric Hermite functions with two shape parameters is proposed. Based on these Hermite functions, new improved first class of Side-Side (FCSS), second class of Side-Side (SCSS), first class of Side-Vertex (FCSV) and second class of Side-Vertex (SCSV) interpolation operators are proposed respectively, which can be used to construct C1 Coons surfaces over triangular domain. By altering the values of two shape parameters, the shape of the Coons surface patch can be adjusted flexibly, but without affecting the function values and partial derivatives of the boundaries. For constructing the triangular surface patches with the center of mass passing through a fixed point, we also give a center of mass function value control method, by which we can solve the corresponding shape parameter values. Moreover, we also apply these four improved interpolation operators to image interpolation. Compared with some widely used image interpolation methods, our methods achieve competitive performance.

Attack Graph Modeling for Implantable Pacemaker.

Remote health monitoring systems are used to audit implantable medical devices or patients' health in a non-clinical setting. These systems are prone to cyberattacks exploiting their critical vulnerabilities. Thus, threatening patients' health and confidentiality. In this paper, a pacemaker automatic remote monitoring system (PARMS) is modeled using architecture analysis and design language (AADL), formally characterized, and checked using the JKind model checker tool. The generated attack graph is visualized using the Graphviz tool, and classifies security breaches through the violation of the security features of significance. The developed attack graph showed the essentiality of setting up appropriate security measures in PARMS.

FlexGraph: Flexible partitioning and storage for scalable graph mining.

How can we analyze large graphs such as the Web, and social networks with hundreds of billions of vertices and edges? Although many graph mining systems have been proposed to perform various graph mining algorithms on such large graphs, they have difficulties in processing Web-scale graphs due to massive communication and I/O costs caused by communication between workers, and reading subgraphs repeatedly. In this paper, we propose FlexGraph, a scalable distributed graph mining method reducing the costs by exploiting properties of real-world graphs. FlexGraph significantly decreases the communication cost, which is the main bottleneck of distributed systems, by exploiting different edge placement policies based on types of vertices. Furthermore, we propose a flexible storage format to reduce I/O costs when reading input graph repeatedly. Experiments show that FlexGraph succeeds in processing up to 64× larger graphs than existing distributed memory-based graph mining methods, and consistently outperforms previous disk-based graph mining methods.

Performance of primary diagnostic monitors (PDMs) over time.

In this work, we evaluated the change of primary monitor characteristics in two consecutive years. Sixty-six primary monitors were included in the analysis. The monitors were located at radiology physicians' offices and radiology reading rooms. All primary monitors were equipped with the manufacturer's built-in photometers and connected to the BarcoMediCalQA web service for manual and automatic quality control measurements. External photometer/illuminance meter (RaySafe Solo Light) was used to measure the luminance values. Measured luminance values of the TG18LN1-18 and TG18UNL80 test patterns were used to evaluate the primary monitors performance. In a comparison of the quality assurance (QA) measurement results for the same monitors that were performed within 2 years, the luminance of 25 displays remained statistically the same (P > 0.01). The luminance of 17 displays decreased (P < 0.01) in 2017 when compared with 2016, the luminance of 24 displays increased (P < 0.01) in 2017 when compared with 2016. For the annual measurements of the MLD in 2016 and 2017, 25 out of 66 displays showed a decrease of MLD values in 2017 compared with the same measurements in 2016 and 41 displays showed an increase of MLD in 2017. All tested primary displays had the MLD value less than 17.2%. The mean value of illuminance measured in 2016 was 5.8 lux ± 3.1 lux. In 2017, the mean value of illuminance measured was 8.7 lux ± 5.3 lux. Although it is expected that monitors luminance values will decrease over time, we found displays with increased luminance. This is possibly due to the multiple monitor calibrations that were performed between two annual monitor QA tests. Based on the findings of this work, more efficient display QA programs with a shorter time interval than 1 year are needed.

Standardized Evaluation of Cerebral Arteriovenous Malformations Using Flow Distribution Network Graphs and Dual-venc 4D Flow MRI.

BACKGROUND: Cerebral arteriovenous malformations (AVMs) are pathological connections between arteries and veins. Dual-venc 4D flow MRI, an extended 4D flow MRI method with improved velocity dynamic range, provides time-resolved 3D cerebral hemodynamics. PURPOSE: To optimize dual-venc 4D flow imaging parameters for AVM; to assess the relationship between spatial resolution, acceleration, and flow quantification accuracy; and to introduce and apply the flow distribution network graph (FDNG) paradigm for storing and analyzing complex neurovascular 4D flow data. STUDY TYPE: Retrospective cohort study. SUBJECTS/PHANTOM: Scans were performed in a specialized flow phantom: 26 healthy subjects (age 41 ± 17 years) and five AVM patients (age 27-68 years). FIELD STRENGTH/SEQUENCE: Dual-venc 4D flow with varying spatial resolution and acceleration factors were performed at 3T field strength. ASSESSMENT: Quantification accuracy was assessed in vitro by direct comparison to measured flow. FDNGs were used to quantify and compare flow, peak velocity (PV), and pulsatility index (PI) between healthy controls with various Circle of Willis (CoW) anatomy and AVM patients. STATISTICAL TESTS: In vitro measurements were compared to ground truth with Student's t-test. In vivo groups were compared with Wilcoxon rank-sum test and Kruskal-Wallis test. RESULTS: Flow was overestimated in all in vitro experiments, by an average 7.1 ± 1.4% for all measurement conditions. Error in flow measurement was significantly correlated with number of voxels across the channel (P = 3.11 × 10-28 ) but not with acceleration factor (P = 0.74). For the venous-arterial PV and PI ratios, a significant difference was found between AVM nidal and extranidal circulation (P = 0.008 and 0.05, respectively), and between AVM nidal and healthy control circulation (P = 0.005 and 0.003, respectively). DATA CONCLUSION: Dual-venc 4D flow MRI and standardized FDNG analysis might be feasible in clinical applications. Venous-arterial ratios of PV and PI are proposed as network-based biomarkers characterizing AVM nidal hemodynamics. LEVEL OF EVIDENCE: 3 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;50:1718-1730.

Robust authentication for paper-based text documents based on text watermarking technology.

Aiming at the problem of easy tampering and difficult integrity authentication of paper text documents, this paper proposes a robust content authentication method for printed documents based on text watermarking scheme resisting print-and-scan attack. Firstly, an authentication watermark signal sequence related to content of text document is generated based on the Logistic chaotic map model; then, the authentication watermark signal sequence is embedded into printed paper document by using a robust text watermarking scheme; finally, the watermark information is extracted from scanned image of paper document, and compared with the authentication watermark information calculated in real time by the text document content obtained by OCR technology, thereby performing content integrity authentication of the paper text documents. Experimental results show that our method can achieve the robust content integrity authentication of paper text documents, and can also accurately locate the tampering position. In addition, the document after embedding the watermark information has a good visual effect, and the text watermarking scheme has a large information capacity.

Reporting Insulin Pump Accuracy: Trumpet Curves According to IEC 60601-2-24 and Beyond.

Accuracy of insulin pump basal rate delivery, if tested according to the standard IEC 60601-2-24 for infusion pumps, shall be presented as a trumpet curve. This way of graphical presentation is common; however, it is often misunderstood and misinterpreted by people. It is often assumed that a trumpet curve shows the error rate as a function of time, thus implying an increasing accuracy in the course of time. On the contrary, the horizontal axis of a trumpet curve shows increasingly long observation windows. In addition, trumpet curves display only extreme values, that is, those windows with minimal and maximal deviation, which might not be representative for the total deviation. This commentary provides information regarding the calculations and the interpretation of trumpet curves and proposes alternative approaches.

How can we make better graphs? An initiative to increase the graphical expertise and productivity of quantitative scientists.

Graphics are at the core of exploring and understanding data, communicating results and conclusions, and supporting decision-making. Increasing our graphical expertise can significantly strengthen our impact as professional statisticians and quantitative scientists. In this article, we present a concerted effort to improve the way we create graphics at Novartis. We provide our vision and guiding principles, before describing seven work packages in more detail. The actions, principles, and experiences laid out in this paper are applicable generally, also beyond drug development, which is our field of work. The purpose of this article is to share our experiences and help foster the use of good graphs in pharmaceutical statistics and beyond. A Graphics Principles "Cheat Sheet" is available online at https://graphicsprinciples.github.io/.

SBML Level 3 package: Render, Version 1, Release 1.

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). This document describes the SBML Level 3 Render package that complements the SBML Level 3 Layout package and provides a means of capturing the precise rendering of the elements in a diagram. The SBML Level 3 Render package provides a flexible approach to rendering that is independent of both the underlying SBML model and the Layout information. There can be one block of render information that applies to all layouts or an additional block for each layout. Many of the elements used in the current render specification are based on corresponding elements from the SVG specification. This allows us to easily convert a combination of layout information and render information into a SVG drawing.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.0 of SBOL Visual, which builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions and molecular species, making the relationship between diagrams and the SBOL data model explicit, supporting families of symbol variants, clarifying a number of requirements and best practices, and significantly expanding the collection of diagram glyphs.

Data visualization, bar naked: A free tool for creating interactive graphics.

Although bar graphs are designed for categorical data, they are routinely used to present continuous data in studies that have small sample sizes. This presentation is problematic, as many data distributions can lead to the same bar graph, and the actual data may suggest different conclusions from the summary statistics. To address this problem, many journals have implemented new policies that require authors to show the data distribution. This paper introduces a free, web-based tool for creating an interactive alternative to the bar graph (http://statistika.mfub.bg.ac.rs/interactive-dotplot/). This tool allows authors with no programming expertise to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of a continuous variable across different study groups. Individual data points may be overlaid on the graphs. Additional features facilitate visualization of subgroups or clusters of non-independent data. A second tool enables authors to create interactive graphics from data obtained with repeated independent experiments (http://statistika.mfub.bg.ac.rs/interactive-repeated-experiments-dotplot/). These tools are designed to encourage exploration and critical evaluation of the data behind the summary statistics and may be valuable for promoting transparency, reproducibility, and open science in basic biomedical research.

Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language.

The Beacon Editor is a cross-platform desktop application for the creation and modification of signal transduction pathways using the Systems Biology Graphical Notation Activity Flow (SBGN-AF) language. Prompted by biologists' requests for enhancements, the Beacon Editor includes numerous powerful features for the benefit of creation and presentation.