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.

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.

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.

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.

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/.

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.

An Evaluation of Performance Characteristics of Primary Display Devices.

The aim of this study was to complete a full evaluation of the new EIZO RX850 liquid crystal display and compare it to two currently used medical displays in Australia (EIZO GS510 and Barco MDCG 5121). The American Association of Physicists in Medicine (AAPM) Task Group 18 Quality Control test pattern was used to assess the performance of three high-resolution primary medical displays: EIZO RX850, EIZO GS510, and Barco MDCG 5121. A Konica Minolta spectroradiometer (CS-2000) was used to assess luminance response, non-uniformity, veiling glare, and color uniformity. Qualitative evaluation of noise was also performed. Seven breast lesions were displayed on each monitor and photographed with a calibrated 5.5-MP Olympus E-1 digital SLR camera. ImageJ software was used to sample pixel information from each lesion and surrounding background to calculate their conspicuity index on each of the displays. All monitor fulfilled all AAPM acceptance criteria. The performance characteristics for EIZO RX850, Barco MDCG 5121, and EIZO GS510 respectively were as follows: maximum luminance (490, 500.5, and 413 cd/m(2)), minimum luminance (0.724, 1.170, and 0.92 cd/m(2)), contrast ratio (675:1, 428:1, 449:1), just-noticeable difference index (635, 622, 609), non-uniformity (20, 5.92, and 8.5 %), veiling glare (GR = 2465.6, 720.4, 1249.8), and color uniformity (Δu'v' = +0.003, +0.002, +0.002). All monitors demonstrated low noise levels. The conspicuity index (χ) of the lesions was slightly higher in the EIZO RX850 display. All medical displays fulfilled AAPM performance criteria, and performance characteristics of EIZO RX850 are equal to or better than those of the Barco MDCG 5121 and EIZO GS510 displays.

Seeing is believing: good graphic design principles for medical research.

Have you noticed when you browse a book, journal, study report, or product label how your eye is drawn to figures more than to words and tables? Statistical graphs are powerful ways to transparently and succinctly communicate the key points of medical research. Furthermore, the graphic design itself adds to the clarity of the messages in the data. The goal of this paper is to provide a mechanism for selecting the appropriate graph to thoughtfully construct quality deliverables using good graphic design principles. Examples are motivated by the efforts of a Safety Graphics Working Group that consisted of scientists from the pharmaceutical industry, Food and Drug Administration, and academic institutions.

Visualizing simulated electrical fields from electroencephalography and transcranial electric brain stimulation: a comparative evaluation.

Electrical activity of neuronal populations is a crucial aspect of brain activity. This activity is not measured directly but recorded as electrical potential changes using head surface electrodes (electroencephalogram - EEG). Head surface electrodes can also be deployed to inject electrical currents in order to modulate brain activity (transcranial electric stimulation techniques) for therapeutic and neuroscientific purposes. In electroencephalography and noninvasive electric brain stimulation, electrical fields mediate between electrical signal sources and regions of interest (ROI). These fields can be very complicated in structure, and are influenced in a complex way by the conductivity profile of the human head. Visualization techniques play a central role to grasp the nature of those fields because such techniques allow for an effective conveyance of complex data and enable quick qualitative and quantitative assessments. The examination of volume conduction effects of particular head model parameterizations (e.g., skull thickness and layering), of brain anomalies (e.g., holes in the skull, tumors), location and extent of active brain areas (e.g., high concentrations of current densities) and around current injecting electrodes can be investigated using visualization. Here, we evaluate a number of widely used visualization techniques, based on either the potential distribution or on the current-flow. In particular, we focus on the extractability of quantitative and qualitative information from the obtained images, their effective integration of anatomical context information, and their interaction. We present illustrative examples from clinically and neuroscientifically relevant cases and discuss the pros and cons of the various visualization techniques.

Visual analysis in single case experimental design studies: brief review and guidelines.

Visual analysis of graphic displays of data is a cornerstone of studies using a single case experimental design (SCED). Data are graphed for each participant during a study with trend, level, and stability of data assessed within and between conditions. Reliable interpretations of effects of an intervention are dependent on researchers' understanding and use of systematic procedures. The purpose of this paper is to provide readers with a rationale for visual analysis of data when using a SCED, a step-by-step guide for conducting a visual analysis of graphed data, as well as to highlight considerations for persons interested in using visual analysis to evaluate an intervention, especially the importance of collecting reliability data for dependent measures and fidelity of implementation of study procedures.

Two-layer fragile watermarking method secured with chaotic map for authentication of digital Holy Quran.

This paper presents a novel watermarking method to facilitate the authentication and detection of the image forgery on the Quran images. Two layers of embedding scheme on wavelet and spatial domain are introduced to enhance the sensitivity of fragile watermarking and defend the attacks. Discrete wavelet transforms are applied to decompose the host image into wavelet prior to embedding the watermark in the wavelet domain. The watermarked wavelet coefficient is inverted back to spatial domain then the least significant bits is utilized to hide another watermark. A chaotic map is utilized to blur the watermark to make it secure against the local attack. The proposed method allows high watermark payloads, while preserving good image quality. Experiment results confirm that the proposed methods are fragile and have superior tampering detection even though the tampered area is very small.

Preventing shoulder-surfing attack with the concept of concealing the password objects' information.

Traditionally, picture-based password systems employ password objects (pictures/icons/symbols) as input during an authentication session, thus making them vulnerable to "shoulder-surfing" attack because the visual interface by function is easily observed by others. Recent software-based approaches attempt to minimize this threat by requiring users to enter their passwords indirectly by performing certain mental tasks to derive the indirect password, thus concealing the user's actual password. However, weaknesses in the positioning of distracter and password objects introduce usability and security issues. In this paper, a new method, which conceals information about the password objects as much as possible, is proposed. Besides concealing the password objects and the number of password objects, the proposed method allows both password and distracter objects to be used as the challenge set's input. The correctly entered password appears to be random and can only be derived with the knowledge of the full set of password objects. Therefore, it would be difficult for a shoulder-surfing adversary to identify the user's actual password. Simulation results indicate that the correct input object and its location are random for each challenge set, thus preventing frequency of occurrence analysis attack. User study results show that the proposed method is able to prevent shoulder-surfing attack.

[To explain is to narrate. How to visualize scientific data]. / Spiegare è narrare. Come visualizzare dati scientifici.

When you try to appeal a vast ranging audience, as it occurs at the New Scientist that addresses scientists as well as the general public, your scientific visual explainer must be succinct, clear, accurate and easily understandable. In order to reach this goal, your message should provide only the main data, the ones that allow you to balance information and clarity: information should be put into context and all the extra details should be cut down. It is very important, then, to know well both your audience and the subject you are going to describe, as graphic masters of the past, like William Playfair and Charles Minard, have taught us. Moreover, you should try to engage your reader connecting the storytelling power of words and the driving force of the graphics: colours, visual elements, typography. To be effective, in fact, an infographic should not only be truthful and functional, but also elegant, having style and legibility.