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Ever-increasing availability of experimental volumetric data (e.g., in .ccp4, .mrc, .map, .rec, .zarr, .ome.tif formats) and advances in segmentation software (e.g., Amira, Segger, IMOD) and formats (e.g., .am, .seg, .mod, etc.) have led to a demand for efficient web-based visualization tools. Despite this, current solutions remain scarce, hindering data interpretation and dissemination. Previously, we introduced Mol* Volumes & Segmentations (Mol* VS), a web application for the visualization of volumetric, segmentation, and annotation data (e.g., semantically relevant information on biological entities corresponding to individual segmentations such as Gene Ontology terms or PDB IDs). However, this lacked important features such as the ability to edit annotations (e.g., assigning user-defined descriptions of a segment) and seamlessly share visualizations. Additionally, setting up Mol* VS required a substantial programming background. This article presents an updated version, Mol* VS 2.0, that addresses these limitations. As part of Mol* VS 2.0, we introduce the Annotation Editor, a user-friendly graphical interface for editing annotations, and the Volumes & Segmentations Toolkit (VSToolkit) for generating shareable files with visualization data. The outlined protocols illustrate the utilization of Mol* VS 2.0 for visualization of volumetric and segmentation data across various scales, showcasing the progress in the field of molecular complex visualization. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: VSToolkit-setting up and visualizing a user-constructed Mol* VS 2.0 database entry Basic Protocol 2: VSToolkit-visualizing multiple time frames and volume channels Support Protocol 1: Example: Adding database entry idr-13457537 Alternate Protocol 1: Local-server-and-viewer-visualizing multiple time frames and volume channels Support Protocol 2: Addition of database entry custom-tubhiswt Basic Protocol 3: VSToolkit-visualizing a specific channel and time frame Basic Protocol 4: VSToolkit-visualizing geometric segmentation Basic Protocol 5: VSToolkit-visualizing lattice segmentations Alternate Protocol 2: "Local-server-and-viewer"-visualizing lattice segmentations Basic Protocol 6: "Local-server-and-viewer"-visualizing multiple volume channels Support Protocol 3: Deploying a server API Support Protocol 4: Hosting Mol* viewer with VS extension 2.0 Support Protocol 5: Example: Addition of database entry empiar-11756 Support Protocol 6: Example: Addition of database entry emd-1273 Support Protocol 7: Editing annotations Support Protocol 8: Addition of database entry idr-5025553., (© 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.)

Background and Objective: Numerical simulations are valuable tools for studying cardiac arrhythmias. Not only do they complement experimental studies, but there is also an increasing expectation for their use in clinical applications to guide patient-specific procedures. However, numerical studies that solve the reaction-diffusion equations describing cardiac electrical activity remain challenging to set up, are time-consuming, and in many cases, are prohibitively computationally expensive for long studies. The computational cost of cardiac simulations of complex models on anatomically accurate structures necessitates parallel computing. Graphics processing units (GPUs), which have thousands of cores, have been introduced as a viable technology for carrying out fast cardiac simulations, sometimes including real-time interactivity. Our main objective is to increase the performance and accuracy of such GPU implementations while conserving computational resources., Methods: In this work, we present a compression algorithm that can be used to conserve GPU memory and improve efficiency by managing the sparsity that is inherent in using Cartesian grids to represent cardiac structures directly obtained from high-resolution MRI and mCT scans. Furthermore, we present a discretization scheme that includes the cross-diagonal terms in the computational cell to increase numerical accuracy, which is especially important for simulating thin tissue sections without the need for costly mesh refinement., Results: Interactive WebGL simulations of atrial/ventricular structures (on PCs, laptops, tablets, and phones) demonstrate the algorithm's ability to reduce memory demand by an order of magnitude and achieve calculations up to 20x faster. We further showcase its superiority in slender tissues and validate results against experiments performed in live explanted human hearts., Conclusions: In this work, we present a compression algorithm that accelerates electrical activity simulations on realistic anatomies by an order of magnitude (up to 20x), thereby allowing the use of finer grid resolutions while conserving GPU memory. Additionally, improved accuracy is achieved through cross-diagonal terms, which are essential for thin tissues, often found in heart structures such as pectinate muscles and trabeculae, as well as Purkinje fibers. Our method enables interactive simulations with even interactive domain boundary manipulation (unlike finite element/volume methods). Finally, agreement with experiments and ease of mesh import into WebGL paves the way for virtual cohorts and digital twins, aiding arrhythmia analysis and personalized therapies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier B.V.)

Unsupervised graph learning techniques have garnered increasing interest among researchers. These methods employ the technique of maximizing mutual information to generate representations of nodes and graphs. We show that these methods are susceptible to backdoor attacks, wherein the adversary can poison a small portion of unlabeled graph data (e.g., node features and graph structure) by introducing triggers into the graph. This tampering disrupts the representations and increases the risk to various downstream applications. Previous backdoor attacks in supervised learning primarily operate directly on the label space and may not be suitable for unlabeled graph data. To tackle this challenge, we introduce GRBA, 1 a gradient-based first-order backdoor attack method. To the best of our knowledge, this constitutes a pioneering endeavor in investigating backdoor attacks within the domain of unsupervised graph learning. The initiation of this method does not necessitate prior knowledge of downstream tasks, as it directly focuses on representations. Furthermore, it is versatile and can be applied to various downstream tasks, including node classification, node clustering and graph classification. We evaluate GRBA on state-of-the-art unsupervised learning models, and the experimental results substantiate the effectiveness and evasiveness of GRBA in both node-level and graph-level tasks., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Graph neural networks (GNNs) have achieved state-of-the-art performance in graph representation learning. Message passing neural networks, which learn representations through recursively aggregating information from each node and its neighbors, are among the most commonly-used GNNs. However, a wealth of structural information of individual nodes and full graphs is often ignored in such process, which restricts the expressive power of GNNs. Various graph data augmentation methods that enable the message passing with richer structure knowledge have been introduced as one main way to tackle this issue, but they are often focused on individual structure features and difficult to scale up with more structure features. In this work we propose a novel approach, namely collective structure knowledge-augmented graph neural network (CoS-GNN), in which a new message passing method is introduced to allow GNNs to harness a diverse set of node- and graph-level structure features, together with original node features/attributes, in augmented graphs. In doing so, our approach largely improves the structural knowledge modeling of GNNs in both node and graph levels, resulting in substantially improved graph representations. This is justified by extensive empirical results where CoS-GNN outperforms state-of-the-art models in various graph-level learning tasks, including graph classification, anomaly detection, and out-of-distribution generalization., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Accurate and fast understanding of the patient's anatomy is crucial in surgical decision making and particularly important in visceral surgery. Sophisticated visualization techniques such as 3D Volume Rendering can aid the surgeon and potentially lead to a benefit for the patient. Recently, we proposed a novel volume rendering technique called Adaptive Volumetric Illumination Sampling (AVIS) that can generate realistic lighting in real-time, even for high resolution images and volumes but without introducing additional image noise. In order to evaluate this new technique, we conducted a randomized, three-period crossover study comparing AVIS to conventional Direct Volume Rendering (DVR) and Path Tracing (PT). CT datasets from 12 patients were evaluated by 10 visceral surgeons who were either senior physicians or experienced specialists. The time needed for answering clinically relevant questions as well as the correctness of the answers were analyzed for each visualization technique. In addition to that, the perceived workload during these tasks was assessed for each technique, respectively. The results of the study indicate that AVIS has an advantage in terms of both time efficiency and most aspects of the perceived workload, while the average correctness of the given answers was very similar for all three methods. In contrast to that, Path Tracing seems to show particularly high values for mental demand and frustration. We plan to repeat a similar study with a larger participant group to consolidate the results.

In this article, we propose a novel cascaded diffusion-based generative framework for text-driven human motion synthesis, which exploits a strategy named GradUally Enriching SyntheSis (GUESS as its abbreviation). The strategy sets up generation objectives by grouping body joints of detailed skeletons in close semantic proximity together and then replacing each of such joint group with a single body-part node. Such an operation recursively abstracts a human pose to coarser and coarser skeletons at multiple granularity levels. With gradually increasing the abstraction level, human motion becomes more and more concise and stable, significantly benefiting the cross-modal motion synthesis task. The whole text-driven human motion synthesis problem is then divided into multiple abstraction levels and solved with a multi-stage generation framework with a cascaded latent diffusion model: an initial generator first generates the coarsest human motion guess from a given text description; then, a series of successive generators gradually enrich the motion details based on the textual description and the previous synthesized results. Notably, we further integrate GUESS with the proposed dynamic multi-condition fusion mechanism to dynamically balance the cooperative effects of the given textual condition and synthesized coarse motion prompt in different generation stages. Extensive experiments on large-scale datasets verify that GUESS outperforms existing state-of-the-art methods by large margins in terms of accuracy, realisticness, and diversity.

The increasing ubiquity of data in everyday life has elevated the importance of data literacy and accessible data representations, particularly for individuals with disabilities. While prior research predominantly focuses on the needs of the visually impaired, our survey aims to broaden this scope by investigating accessible data representations across a more inclusive spectrum of disabilities. After conducting a systematic review of 152 accessible data representation papers from ACM and IEEE databases, we found that roughly 78% of existing articles center on vision impairments. In this article, we conduct a comprehensive review of the remaining 22% of papers focused on underrepresented disability communities. We developed categorical dimensions based on accessibility, visualization, and human-computer interaction to classify the papers. These dimensions include the community of focus, issues addressed, contribution type, study methods, participants involved, data type, visualization type, and data domain. Our work redefines accessible data representations by illustrating their application for disabilities beyond those related to vision. Building on our literature review, we identify and discuss opportunities for future research in accessible data representations.

This article, from the perspective of structural features, focuses on in-car user interface icons and explores the impact of different icon structural features on visual search efficiency. Initially, we categorised the icons into four groups based on structural features: individual structure icons (ISI), enclosed structure icons (ESI), horizontal structure icons (HSI) and vertical structure icons (VSI). Subsequently, we conducted a visual search experiment with structure as the sole variable, recording participants' behaviours and eye-tracking data. Finally, data analysis was conducted using methods including analysis of variance and logistic regression. The results indicate that differences in icon structural features significantly affect visual search efficiency, showcasing significant intergroup differences. HSI exhibit the highest visual search efficiency, while ESI show the lowest efficiency. ISI have shorter response times but the lowest matching accuracy. VSI only perform better than ESI. These findings hold significant implications for optimising icon design and enhancing visual search efficiency.

Advances in haptic technology have led researchers and engineers to seek out killer applications in which users can enjoy an experience of touch in AR/VR spaces. Such applications will respond appropriately to human desire for haptic experiences (i.e., touch desire) and thus it is essential for researchers and engineers to understand the nature of people's touch desires as they arise in the course of daily life. In this study, we employed Twitter data analysis to investigate a diurnal pattern in touch desire. Our results showed that touch desire identified in and extracted from Twitter texts did reveal a diurnal pattern. Touch desire tended to be at its lowest in the morning and increased as the day progressed. The time at which it peaked varied with the specific target of touch desire. Touch desire in relation to other people and objects reached its peak at night, but touch desire in relation to animals reached its peak at noon. These results were confirmed not only by our Twitter text analysis but also by data from other social media and an online survey. In addition, we found that the diurnal pattern of touch desire for each target shows a strong correlation with that of visual desire for the same target. This suggests that the diurnal pattern of touch desire is not limited to the sense of touch but is common to other sensory desires for each target. Our findings suggest that researchers need to take the time of day into account when investigating touch desire. Our findings also offer valuable insights for developers into the design of haptic applications and displays that takes into account the timing of daily peaks in touch desire.

Molecular docking is an essential tool in structure-based drug discovery, widely utilized to model ligand-protein interactions and enrich potential hits. Among the different docking strategies, semiflexible docking (rigid-receptor and flexible-ligand model) is the most popular, benefiting from its balance of docking accuracy and speed. However, this approach ignores the conformational changes of proteins and hence demands suitable protein conformations as input. When the binding interaction adheres to an induced-fit model, flexible methods such as molecular dynamics simulation can be utilized, but they are computationally demanding. To balance between speed and accuracy, the flexible docking approach is an effective choice, as exemplified by AutoDock Vina and AutoDockFR, which treat selected protein side chains as flexible parts. However, the efficiency of flexible docking methods is yet to be improved for virtual screening usage. In this article, we introduce DSDPFlex, an improved flexible-receptor docking method accelerated by GPU parallelization. Beyond acceleration, optimizations with respect to sampling, scoring, and search space are implemented in DSDPFlex to further improve its capability in flexible tasks. In cross-docking evaluation, DSDPFlex demonstrates superior accuracy compared to AutoDock Vina and is 100 times faster than Vina in flexible-receptor tasks. We also show the advantage of flexible-receptor methods on suboptimal pockets and validate the advantage of DSDPFlex in screening on apo and AlphaFold2-predicted structures. With improvements in both efficiency and accuracy, DSDPFlex is expected to hold potential in future docking-based studies.

Alchemical free energy campaigns can be planned using graph theory by building networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce Konnektor, an open-source Python package, for systematically planning, modifying, and analyzing free energy calculation networks. Konnektor is designed to aid in the drug discovery process by enabling users to easily setup free energy campaigns using complex graph manipulation methods. The package contains functions for network operations including concatenation of networks, deletion of transformations, and clustering of molecules along with a framework for combining these tools with existing network generation algorithms to enable the development of more complex methods for network generation. A comparison of the various network layout features offered is carried out using toy data sets. Additionally, Konnektor contains visualization and analysis tools, making the investigation of network features much simpler. Besides the content of the package, the paper also offers application examples, demonstrating how Konnektor can be used and how the different networks perform from a graph theory perspective. Konnektor is freely available via GitHub at https://github.com/OpenFreeEnergy/konnektor under the permissive MIT License.

Graph neural networks (GNNs) have revolutionized drug discovery in chemistry and biology, enhancing efficiency and reducing resource demands. However, classical GNNs often struggle to capture long-range dependencies due to challenges like oversmoothing and oversquashing. Graph Transformers address these issues by employing global self-attention mechanisms that allow direct information exchange between any pair of nodes, enabling the modeling of long-range interactions. Despite this, Graph Transformers often face difficulties in capturing the nuanced structural information on graphs. To overcome these challenges, we introduce the CurvFlow-Transformer, a novel graph Transformer model incorporating a curvature flow-based masked attention mechanism. By leveraging a topologically enhanced mask matrix, the attention layer can effectively detect subtle structural differences within graphs, balancing the focus between global mutual information and local structural details of molecules. The CurvFlow-Transformer demonstrates superior performance on the MoleculeNet data set, surpassing several state-of-the-art models across various tasks. Moreover, the model provides unique insights into the relationship between molecular structure and chemical properties by analyzing the attention heat coefficients of individual atoms.

Background: The maximal sensitivity for local pairwise alignment makes the Smith-Waterman algorithm a popular choice for protein sequence database search. However, its quadratic time complexity makes it compute-intensive. Unfortunately, current state-of-the-art software tools are not able to leverage the massively parallel processing capabilities of modern GPUs with close-to-peak performance. This motivates the need for more efficient implementations., Results: CUDASW++4.0 is a fast software tool for scanning protein sequence databases with the Smith-Waterman algorithm on CUDA-enabled GPUs. Our approach achieves high efficiency for dynamic programming-based alignment computation by minimizing memory accesses and instructions. We provide both efficient matrix tiling, and sequence database partitioning schemes, and exploit next generation floating point arithmetic and novel DPX instructions. This leads to close-to-peak performance on modern GPU generations (Ampere, Ada, Hopper) with throughput rates of up to 1.94 TCUPS, 5.01 TCUPS, 5.71 TCUPS on an A100, L40S, and H100, respectively. Evaluation on the Swiss-Prot, UniRef50, and TrEMBL databases shows that CUDASW++4.0 gains over an order-of-magnitude performance improvements over previous GPU-based approaches (CUDASW++3.0, ADEPT, SW#DB). In addition, our algorithm demonstrates significant speedups over top-performing CPU-based tools (BLASTP, SWIPE, SWIMM2.0), can exploit multi-GPU nodes with linear scaling, and features an impressive energy efficiency of up to 15.7 GCUPS/Watt., Conclusion: CUDASW++4.0 changes the standing of GPUs in protein sequence database search with Smith-Waterman alignment by providing close-to-peak performance on modern GPUs. It is freely available at https://github.com/asbschmidt/CUDASW4 ., (© 2024. The Author(s).)

Network meta-analysis (NMA) incorporates all available evidence into a general statistical framework for comparing multiple treatments. Standard NMAs make three major assumptions, namely homogeneity, similarity, and consistency, and violating these assumptions threatens an NMA's validity. In this article, we suggest a graphical approach to assessing these assumptions and distinguishing between qualitative and quantitative versions of these assumptions. In our plot, the absolute effect of each treatment arm is plotted against the level of effect modifiers, and the three assumptions of NMA can then be visually evaluated. We use four hypothetical scenarios to show how violating these assumptions can lead to different consequences and difficulties in interpreting an NMA. We present an example of an NMA evaluating steroid use to treat septic shock patients to demonstrate how to use our graphical approach to assess an NMA's assumptions and how this approach can help with interpreting the results. We also show that all three assumptions of NMA can be summarized as an exchangeability assumption. Finally, we discuss how reporting of NMAs can be improved to increase transparency of the analysis and interpretability of the results., (© 2024 The Author(s). Research Synthesis Methods published by John Wiley & Sons Ltd.)

Our work investigates the influence of self-related cues in the design of virtual humans on body perception in virtual reality. In a $2\times 2$ mixed design, 64 participants faced photorealistic virtual humans either as a motion-synchronized embodied avatar or as an autonomous moving agent, appearing subsequently with a personalized and generic texture. Our results unveil that self-related cues through embodiment and personalization yield an individual and complemented increase in participants' sense of embodiment and self-identification towards the virtual human. Different body weight modification and estimation tasks further showed an impact of both factors on participants' body weight perception. Additional analyses revealed that the participant's body mass index predicted body weight estimations in all conditions and that participants' self-esteem and body shape concerns correlated with different body weight perception results. Hence, we have demonstrated the occurrence of double standards through induced self-related cues in virtual human perception, especially through embodiment.

Mixed Reality allows us to integrate virtual and physical content into users' environments seamlessly. Yet, how this fusion affects perceptual and cognitive resources and our ability to find virtual or physical objects remains uncertain. Displaying virtual and physical information simultaneously might lead to divided attention and increased visual complexity, impacting users' visual processing, performance, and workload. In a visual search task, we asked participants to locate virtual and physical objects in Augmented Reality and Augmented Virtuality to understand the effects on performance. We evaluated search efficiency and attention allocation for virtual and physical objects using event-related potentials, fixation and saccade metrics, and behavioral measures. We found that users were more efficient in identifying objects in Augmented Virtuality, while virtual objects gained saliency in Augmented Virtuality. This suggests that visual fidelity might increase the perceptual load of the scene. Reduced amplitude in distractor positivity ERP, and fixation patterns supported improved distractor suppression and search efficiency in Augmented Virtuality. We discuss design implications for mixed reality adaptive systems based on physiological inputs for interaction.

We present HOIMotion - a novel approach for human motion forecasting during human-object interactions that integrates information about past body poses and egocentric 3D object bounding boxes. Human motion forecasting is important in many augmented reality applications but most existing methods have only used past body poses to predict future motion. HOIMotion first uses an encoder-residual graph convolutional network (GCN) and multi-layer perceptrons to extract features from body poses and egocentric 3D object bounding boxes, respectively. Our method then fuses pose and object features into a novel pose-object graph and uses a residual-decoder GCN to forecast future body motion. We extensively evaluate our method on the Aria digital twin (ADT) and MoGaze datasets and show that HOIMotion consistently outperforms state-of-the-art methods by a large margin of up to 8.7% on ADT and 7.2% on MoGaze in terms of mean per joint position error. Complementing these evaluations, we report a human study (N=20) that shows that the improvements achieved by our method result in forecasted poses being perceived as both more precise and more realistic than those of existing methods. Taken together, these results reveal the significant information content available in egocentric 3D object bounding boxes for human motion forecasting and the effectiveness of our method in exploiting this information.

We explored the impact of depth of knowledge on conversational agents and human perceptions in a virtual reality (VR) environment. We designed experimental conditions with low, medium, and high depths of knowledge in the domain of game development and tested them among 27 game development students. We aimed to understand how the agent's predefined knowledge levels affected the participants' perceptions of the agent and its knowledge. Our findings showed that participants could distinguish between different knowledge levels of the virtual agent. Moreover, the agent's depth of knowledge significantly impacted participants' perceptions of intelligence, rapport, factuality, the uncanny valley effect, anthropomorphism, and willingness for future interaction. We also found strong correlations between perceived knowledge, perceived intelligence, factuality, and willingness for future interactions. We developed design guidelines for creating conversational agents from our data and observations. This study contributes to the human-agent interaction field in VR settings by providing empirical evidence on the importance of tailoring virtual agents' depth of knowledge to improve user experience, offering insights into designing more engaging and effective conversational agents.

Virtual reality (VR) can potentially enhance student engagement and memory retention in the classroom. However, distraction among participants in a VR-based classroom is a significant concern. Several factors, including mind wandering, external noise, stress, etc., can cause students to become internally and/or externally distracted while learning. To detect distractions, single or multi-modal features can be used. A single modality is found to be insufficient to detect both internal and external distractions, mainly because of individual variability. In this work, we investigated multi-modal features: eye tracking and EEG data, to classify the internal and external distractions in an educational VR environment. We set up our educational VR environment and equipped it for multi-modal data collection. We implemented different machine learning (ML) methods, including k-nearest-neighbors (kNN), Random Forest (RF), one-dimensional convolutional neural network - long short-term memory (1 D-CNN-LSTM), and two-dimensional convolutional neural networks (2D-CNN) to classify participants' internal and external distraction states using the multi-modal features. We performed cross-subject, cross-session, and gender-based grouping tests to evaluate our models. We found that the RF classifier achieves the highest accuracy over 83% in the cross-subject test, around 68% to 78% in the cross-session test, and around 90% in the gender-based grouping test compared to other models. SHAP analysis of the extracted features illustrated greater contributions from the occipital and prefrontal regions of the brain, as well as gaze angle, gaze origin, and head rotation features from the eye tracking data.

With eye tracking finding widespread utility in augmented reality and virtual reality headsets, eye gaze has the potential to recognize users' visual tasks and adaptively adjust virtual content displays, thereby enhancing the intelligence of these headsets. However, current studies on visual task recognition often focus on scene-specific tasks, like copying tasks for office environments, which lack applicability to new scenarios, e.g., museums. In this paper, we propose four scene-agnostic task types for facilitating task type recognition across a broader range of scenarios. We present a new dataset that includes eye and head movement data recorded from 20 participants while they engaged in four task types across 15 360-degree VR videos. Using this dataset, we propose an egocentric gaze-aware task type recognition method, TRCLP, which achieves promising results. Additionally, we illustrate the practical applications of task type recognition with three examples. Our work offers valuable insights for content developers in designing task-aware intelligent applications. Our dataset and source code are available at zhimin-wang.github.io/TaskTypeRecognition.html.

Neuron tracing, alternately referred to as neuron reconstruction, is the procedure for extracting the digital representation of the three-dimensional neuronal morphology from stacks of microscopic images. Achieving accurate neuron tracing is critical for profiling the neuroanatomical structure at single-cell level and analyzing the neuronal circuits and projections at whole-brain scale. However, the process often demands substantial human involvement and represents a nontrivial task. Conventional solutions towards neuron tracing often contend with challenges such as non-intuitive user interactions, suboptimal data generation throughput, and ambiguous visualization. In this paper, we introduce a novel method that leverages the power of extended reality (XR) for intuitive and progressive semi-automatic neuron tracing in real time. In our method, we have defined a set of interactors for controllable and efficient interactions for neuron tracing in an immersive environment. We have also developed a GPU-accelerated automatic tracing algorithm that can generate updated neuron reconstruction in real time. In addition, we have built a visualizer for fast and improved visual experience, particularly when working with both volumetric images and 3D objects. Our method has been successfully implemented with one virtual reality (VR) headset and one augmented reality (AR) headset with satisfying results achieved. We also conducted two user studies and proved the effectiveness of the interactors and the efficiency of our method in comparison with other approaches for neuron tracing.

Cybersickness continues to bar many individuals from taking full advantage of virtual reality (VR) technology. Previous work has established that navigating virtual terrain with elevation changes poses a significant risk in this regard. In this paper, we investigate the effectiveness of three cybersickness reduction strategies on users performing a navigation task across virtual elevation-altering terrain. These strategies include static field of view (FOV) reduction, a flat surface approach that disables terrain collision and maintains constant elevation for users, and SmoothRide, a novel technique designed to dampen a user's perception of vertical motion as they travel. To assess the impact of these strategies, we conducted a within-subjects study involving 61 participants. Each strategy was compared against a control condition, where users navigated across terrain without any cybersickness reduction measures in place. Cybersickness data were collected using the Fast Motion Sickness Scale (FMS) and Simulator Sickness Questionnaire (SSQ), along with galvanic skin response (GSR) data. We measured user presence using the IGroup Presence questionnaire (IPQ) and a Single-Item Presence Scale (SIP). Our findings reveal that users experienced significantly lower levels of cybersickness using SmoothRide or FOV reduction. Presence scores reported on the IPQ were statistically similar between SmoothRide and the control condition. Conversely, terrain flattening had adverse effects on user presence scores, and we could not identify a significant effect on cybersickness compared to the control. We demonstrate that SmoothRide is an effective, lightweight, configurable, and easy-to-integrate tool for reducing cybersickness in simulations featuring elevation-altering terrain.

Images and videos are widely used to elicit emotions; however, their visual appeal differs from real-world experiences. With virtual reality becoming more realistic, immersive, and interactive, we envision virtual environments to elicit emotions effectively, rapidly, and with high ecological validity. This work presents the first interactive virtual reality dataset to elicit emotions. We created five interactive virtual environments based on corresponding validated 360° videos and validated their effectiveness with 160 participants. Our results show that our virtual environments successfully elicit targeted emotions. Compared with the existing methods using images or videos, our dataset allows virtual reality researchers and practitioners to integrate their designs effectively with emotion elicitation settings in an immersive and interactive way.

Enabled by the latest achievements in artificial intelligence (AI), computer graphics as well as virtual, augmented, and mixed reality (VR/AR/MR), virtual agents are increasingly resembling humans in both their appearance and intelligent behavior. This results in enormous potential for agents to support users in their daily lives, for example in customer service, healthcare, education or the envisioned all-encompassing metaverse. Today's technology would allow users to customize their conversation partners in the metaverse - as opposed to reality - according to their preferences, potentially improving the user experience. On the other hand, there is little research on how reshaping the head of a communication partner might affect the immediate interaction with them. In this paper, we investigate the user requirements for and the effects of agent customization. In a two-stage user study ($N=30$), we collected both self-reported evaluations (e.g., intrinsic motivation) and interaction metrics (e.g., interaction duration and number of tried out items) for the process of agent customization itself as well as data on how users perceived the subsequent human-agent interaction in VR. Our results indicate that users only wish to have full customization for agents in their personal social circle, while for general services, a selection or even a definite assignment of pre-configured agents is sufficient. When customization is offered, attributes such as gender, clothing or hair are subjectively more relevant to users than facial features such as skin or eye color. Although the customization of human interaction partners is beyond our control, customization of virtual agents significantly increases perceived social presence as well as rapport and trust. Further findings on user motivation and agent diversity are discussed in the paper.

Virtual Reality (VR) systems are widely used, and it is essential to know if spatial perception in virtual environments (VEs) is similar to reality. Research indicates that users tend to underestimate distances in VR. Prior work suggests that actual distance judgments in VR may not always match the users self-reported preference of where they think they most accurately estimated distances. However, no explicit investigation evaluated whether user preferences match actual performance in a spatial judgment task. We used blind walking to explore potential dissimilarities between actual distance estimates and user-selected preferences of visual complexities, VE conditions, and targets. Our findings show a gap between user preferences and actual performance when visual complexities were varied, which has implications for better visual perception understanding, VR applications design, and research in spatial perception, indicating the need to calibrate and align user preferences and true spatial perception abilities in VR.

Virtual Reality (VR) has become an important tool for conducting behavioral studies in realistic, reproducible environments. In this paper, we present ISA, an Immersive Study Analyzer system designed for the comprehensive analysis of social VR studies. For in-depth analysis of participant behavior, ISA records all user actions, speech, and the contextual environment of social VR studies. A key feature is the ability to review and analyze such immersive recordings collaboratively in VR, through support of behavioral coding and user-defined analysis queries for efficient identification of complex behavior. Respatialization of the recorded audio streams enables analysts to follow study participants' conversations in a natural and intuitive way. To support phases of close and loosely coupled collaboration, ISA allows joint and individual temporal navigation, and provides tools to facilitate collaboration among users at different temporal positions. An expert review confirms that ISA effectively supports collaborative immersive analysis, providing a novel and effective tool for nuanced understanding of user behavior in social VR studies.

The use of Virtual Reality (VR) technology, especially in medical rehabilitation, has expanded to include tactile cues along with visual stimuli. For patients with upper limb hemiplegia, tangible handles with haptic stimuli could improve their ability to perform daily activities. Traditional VR controllers are unsuitable for patient rehabilitation in VR, necessitating the design of specialized tangible handles with integrated tracking devices. Besides, matching tactile stimulation with corresponding virtual visuals could strengthen users' embodiment (i.e., owning and controlling virtual bodies) in VR, which is crucial for patients' training with virtual hands. Haptic stimuli have been shown to amplify the embodiment in VR, whereas the effect of partial tactile stimulation from tangible handles on embodiment remains to be clarified. This research, including three experiments, aims to investigate how partial tactile feedback of tangible handles impacts users' embodiment, and we proposed a design concept called TouchMark for partial tactile stimuli that could help users quickly connect the physical and virtual worlds. To evaluate users' tactile and comfort perceptions when grasping tangible handles in a non-VR setting, various handles with three partial tactile factors were manipulated in Study 1. In Study 2, we explored the effects of partial feedback using three forms of TouchMark on the embodiment of healthy users in VR, with various tangible handles, while Study 3 focused on similar investigations with patients. These handles were utilized to complete virtual food preparation tasks. The tactile and comfort perceptions of tangible handles and users' embodiment were evaluated in this research using questionnaires and interviews. The results indicate that TouchMark with haptic line and ring forms over no stimulation would significantly enhance users' embodiment, especially for patients. The low-cost and innovative TouchMark approach may assist users, particularly those with limited VR experience, in achieving the embodiment and enhancing their virtual interactive experience.

Cybersickness remains a major drawback of Virtual Reality (VR) headsets, as a breadth of stationary experiences with visual self-motion can result in visually-induced motion sickness. However, not everybody experiences the same intensity or type of adverse symptoms. Here we propose that prior experience with virtual environments can predict ones degree of cybersickness. Video gaming can enhance visuospatial abilities, which in-turn relate negatively to cybersickness - meaning that consistently engaging in virtual environments can result in protective habituation effects. In a controlled stationary VR experiment, we found that 'VR-naive' video gamers experienced significantly less cybersickness in a virtual tunnel-travel task and outperformed 'VR-naive' non-video gamers on a visual attention task. These findings strongly motivate the use of non-VR games for training VR cybersickness resilience, with future research needed to further understand the mechanism(s) by which gamers become cybersickness resilient - potentially expanding access to VR for even the most susceptible participants.

Control over an avatar in virtual reality can improve one's perceived sense of agency and embodiment towards their avatar. Yet, the relationship between control on agency and embodiment remains unclear. This work aims to investigate two main ideas: (1) the effectiveness of currently used metrics in measuring agency and embodiment and (2) the relationship between different levels of control on agency, embodiment, and cognitive performance. To do this, we conducted a between-participants user study with three conditions on agency ($\mathrm{n}=57$). Participants embodied an avatar with one of three types of control (i.e., Low - control over head only, Medium - control over head and torso, or High - control over head, torso, and arms) and completed a Stroop test. Our results indicate that the degree of control afforded to participants impacted their embodiment and cognitive performance but, as expected, could not be detected in the self-reported agency scores. Furthermore, our results elucidated further insights into the relationship between control and embodiment, suggesting potential uncanny valley-like effects. Future work should aim to refine agency measures to better capture the effect of differing levels of control and consider other methodologies to measure agency.

Eye tracking filters have been shown to improve accuracy of gaze estimation and input for stationary settings. However, their effectiveness during physical movement remains underexplored. In this work, we compare common online filters in the context of physical locomotion in extended reality and propose alterations to improve them for on-the-go settings. We conducted a computational experiment where we simulate performance of the online filters using data on participants attending visual targets located in world-, path-, and two head-based reference frames while standing, walking, and jogging. Our results provide insights into the filters' effectiveness and factors that affect it, such as the amount of noise caused by locomotion and differences in compensatory eye movements, and demonstrate that filters with saccade detection prove most useful for on-the-go settings. We discuss the implications of our findings and conclude with guidance on gaze data filtering for interaction in extended reality.

Brain-computer interfaces (BCI) are widely used in the field of disability assistance and rehabilitation, and virtual reality (VR) is increasingly used for visual guidance of BCI-MI (motor imagery). Therefore, how to improve the quality of electroencephalogram (EEG) signals for MI in VR has emerged as a critical issue. People can perform MI more easily when they visualize the hand used for visual guidance as their own, and the Rubber Hand Illusion (RHI) can increase people's ownership of the prosthetic hand. We proposed to induce RHI in VR to enhance participants' MI ability and designed five methods of inducing RHI, namely active movement, haptic stimulation, passive movement, active movement mixed with haptic stimulation, and passive movement mixed with haptic stimulation, respectively. We constructed a first-person training scenario to train participants' MI ability through the five induction methods. The experimental results showed that through the training, the participants' feeling of ownership of the virtual hand in VR was enhanced, and the MI ability was improved. Among them, the method of mixing active movement and tactile stimulation proved to have a good effect on enhancing MI. Finally, we developed a BCI system in VR utilizing the above training method, and the performance of the participants improved after the training. This also suggests that our proposed method is promising for future application in BCI rehabilitation systems.

Virtual/augmented reality (VR/AR) devices offer both immersive imagery and sound. With those wide-field cues, we can simultaneously acquire and process visual and auditory signals to quickly identify objects, make decisions, and take action. While vision often takes precedence in perception, our visual sensitivity degrades in the periphery. In contrast, auditory sensitivity can exhibit an opposite trend due to the elevated interaural time difference. What occurs when these senses are simultaneously integrated, as is common in VR applications such as 360° video watching and immersive gaming? We present a computational and probabilistic model to predict VR users' reaction latency to visual-auditory multisensory targets. To this aim, we first conducted a psychophysical experiment in VR to measure the reaction latency by tracking the onset of eye movements. Experiments with numerical metrics and user studies with naturalistic scenarios showcase the model's accuracy and generalizability. Lastly, we discuss the potential applications, such as measuring the sufficiency of target appearance duration in immersive video playback, and suggesting the optimal spatial layouts for AR interface design.

Text entry is a critical capability for any modern computing experience, with lightweight augmented reality (AR) glasses being no exception. Designed for all-day wearability, a limitation of lightweight AR glass is the restriction to the inclusion of multiple cameras for extensive field of view in hand tracking. This constraint underscores the need for an additional input device. We propose a system to address this gap: a ring-based mid-air gesture typing technique, RingGesture, utilizing electrodes to mark the start and end of gesture trajectories and inertial measurement units (IMU) sensors for hand tracking. This method offers an intuitive experience similar to raycast-based mid-air gesture typing found in VR headsets, allowing for a seamless translation of hand movements into cursor navigation. To enhance both accuracy and input speed, we propose a novel deep-learning word prediction framework, Score Fusion, comprised of three key components: a) a word-gesture decoding model, b) a spatial spelling correction model, and c) a lightweight contextual language model. In contrast, this framework fuses the scores from the three models to predict the most likely words with higher precision. We conduct comparative and longitudinal studies to demonstrate two key findings: firstly, the overall effectiveness of RingGesture, which achieves an average text entry speed of 27.3 words per minute (WPM) and a peak performance of 47.9 WPM. Secondly, we highlight the superior performance of the Score Fusion framework, which offers a 28.2% improvement in uncorrected Character Error Rate over a conventional word prediction framework, Naive Correction, leading to a 55.2% improvement in text entry speed for RingGesture. Additionally, RingGesture received a System Usability Score of 83 signifying its excellent usability.

Matching avatar characteristics to a user can impact sense of embodiment (SoE) in YR. However, few studies have examined how participant demographics may interact with these matching effects. We recruited a diverse and racially balanced sample of 78 participants to investigate the differences among participant groups when embodying both demographically matched and unmatched avatars. We found that participant ethnicity emerged as a significant factor, with Asian and Black participants reporting lower total SoE compared to Hispanic participants. Furthermore, we found that user ethnicity significantly influences ownership (a subscale of SoE), with Asian and Black participants exhibiting stronger effects of matched avatar ethnicity compared to White participants. Additionally, Hispanic participants showed no significant differences, suggesting complex dynamics in ethnic-racial identity. Our results also reveal significant main effects of matched avatar ethnicity and gender on SoE, indicating the importance of considering these factors in VR experiences. These findings contribute valuable insights into understanding the complex dynamics shaping VR experiences across different demographic groups.

Forensic investigation is a complex procedure involving experts working together to establish cause of death and report findings to legal authorities. While new technologies are being developed to provide better post-mortem imaging capabilities-including mixed-reality (MR) tools to support 3D visualisation of such data-these tools do not integrate seamlessly into their existing collaborative workflow and report authoring process, requiring extra steps, e.g. to extract imagery from the MR tool and combine with physical autopsy findings for inclusion in the report. Therefore, in this work we design and evaluate a new forensic autopsy report generation workflow and present a novel documentation system using hybrid mixed-reality approaches to integrate visualisation, voice and hand interaction, as well as collaboration and procedure recording. Our preliminary findings indicate that this approach has the potential to improve data management, aid reviewability, and thus, achieve more robust standards. Further, it potentially streamlines report generation and minimise dependency on external tools and assistance, reducing autopsy time and related costs. This system also offers significant potential for education. A free copy of this paper and all supplemental materials are available at https://osf.io/ygfzx.

Background: The Monte Carlo (MC) method is an accurate technique for particle transport calculation due to the precise modeling of physical interactions. Nevertheless, the MC method still suffers from the problem of expensive computational cost, even with graphics processing unit (GPU) acceleration. Our previous works have investigated the acceleration strategies of photon transport simulation for single-energy CT. But for multi-energy CT, conventional individual simulation leads to unnecessary redundant calculation, consuming more time., Purpose: This work proposes a novel GPU-based shared MC scheme (gSMC) to reduce unnecessary repeated simulations of similar photons between different spectra, thereby enhancing the efficiency of scatter estimation in multi-energy x-ray exposures., Methods: The shared MC method selects shared photons between different spectra using two strategies. Specifically, we introduce spectral region classification strategy to select photons with the same initial energy from different spectra, thus generating energy-shared photon groups. Subsequently, the multi-directional sampling strategy is utilized to select energy-and-direction-shared photons, which have the same initial direction, from energy-shared photon groups. Energy-and-direction-shared photons perform shared simulations, while others are simulated individually. Finally, all results are integrated to obtain scatter distribution estimations for different spectral cases., Results: The efficiency and accuracy of the proposed gSMC are evaluated on the digital phantom and clinical case. The experimental results demonstrate that gSMC can speed up the simulation in the digital case by ∼37.8% and the one in the clinical case by ∼20.6%, while keeping the differences in total scatter results within 0.09%, compared to the conventional MC package, which performs an individual simulation., Conclusions: The proposed GPU-based shared MC simulation method can achieve fast photon transport calculation for multi-energy x-ray exposures., (© 2024 American Association of Physicists in Medicine.)

Objectives: We sought to analyze interactive visualizations and animations of health probability data (such as chances of disease or side effects) that have been studied in head-to-head comparisons with either static graphics or numerical communications., Materials and Methods: Secondary analysis of a large systematic review on ways to communicate numbers in health., Results: We group the research to show that 4 types of animated or interactive visualizations have been studied by multiple researchers: those that simulate experience of probabilistic events; those that demonstrate the randomness of those events; those that reduce information overload by directing attention sequentially to different items of information; and those that promote elaborative thinking. Overall, these 4 types of visualizations do not show strong evidence of improving comprehension, risk perception, or health behaviors over static graphics., Discussion: Evidence is not yet strong that interactivity or animation is more effective than static graphics for communicating probabilities in health. We discuss 2 possibilities: that the most effective visualizations haven't been studied, and that the visualizations aren't effective., Conclusion: Future studies should rigorously compare participant performance with novel interactive or animated visualizations against their performance with static visualizations. Such evidence would help determine whether health communicators should emphasize novel interactive visualizations or rely on older forms of visual communication, which may be accessible to broader audiences, including those with limited digital access., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

Objectives: Visual hierarchy underlies all visual design decisions related to information presentation. This manuscript describes the experience of a multidisciplinary health data visualization and software design team in using visual hierarchy to redesign a hereditary colorectal cancer lab report., Materials and Methods: A series of interviews with representative users were conducted to identify target user groups and determine information hierarchy for each user type. Visual elements (eg, size, color, contrast, etc.) were then assigned to mirror the information hierarchy and workflow for each user type., Results: User research identified 2 distinct user groups as consumers of the redesigned lab report. An interactive design employing a 2-level page hierarchy was developed, which stratified the content to support the needs of each user type., Conclusions: The challenges related to displaying the complex nature of digital and personal health data can be addressed by applying foundational design methods such as visual hierarchy., Discussion: Visual hierarchy, a foundational design principle, can be used by visualization teams to clearly and efficiently present complex datasets associated with healthcare., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Objective: The COVID-19 pandemic emphasized the value of geospatial visual analytics for both epidemiologists and the general public. However, systems struggled to encode temporal and geospatial trends of multiple, potentially interacting variables, such as active cases, deaths, and vaccinations. We sought to ask (1) how epidemiologists interact with visual analytics tools, (2) how multiple, time-varying, geospatial variables can be conveyed in a unified view, and (3) how complex spatiotemporal encodings affect utility for both experts and non-experts., Materials and Methods: We propose encoding variables with animated, concentric, hollow circles, allowing multiple variables via color encoding and avoiding occlusion problems, and we implement this method in a browser-based tool called CoronaViz. We conduct task-based evaluations with non-experts, as well as in-depth interviews and observational sessions with epidemiologists, covering a range of tools and encodings., Results: Sessions with epidemiologists confirmed the importance of multivariate, spatiotemporal queries and the utility of CoronaViz for answering them, while providing direction for future development. Non-experts tasked with performing spatiotemporal queries unanimously preferred animation to multi-view dashboards., Discussion: We find that conveying complex, multivariate data necessarily involves trade-offs. Yet, our studies suggest the importance of complementary visualization strategies, with our animated multivariate spatiotemporal encoding filling important needs for exploration and presentation., Conclusion: CoronaViz's unique ability to convey multiple, time-varying, geospatial variables makes it both a valuable addition to interactive COVID-19 dashboards and a platform for empowering experts and the public during future disease outbreaks. CoronaViz is open-source and a live instance is freely hosted at http://coronaviz.umiacs.io., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Stylization of 3D shapes has been a prominent topic in computer graphics. Geometric stylization, as a category within 3D shape stylization, has garnered widespread attention due to its distinctive geometric aesthetics. This paper introduces a novel and simplified method for achieving regular octahedral stylization, capable of transforming the input shape into the regular octahedral style while preserving the content of the original shape. The proposed method achieves regular octahedral stylization by using face normals. Its implementation is straightforward because it incurs a cost only in terms of solving several linear systems. To demonstrate the effectiveness and robustness of the proposed method, extensive tests were conducted on models with varying levels of complexity and topological structures. The results highlight the exceptional capability of the proposed method to generate geometric shapes with an aesthetically pleasing regular octahedral style., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Dong et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Data in behavioral research is often quantified with event-logging software, generating large data sets containing detailed information about subjects, recipients, and the duration of behaviors. Exploring and analyzing such large data sets can be challenging without tools to visualize behavioral interactions between individuals or transitions between behavioral states, yet software that can adequately visualize complex behavioral data sets is rare. TIBA (The Interactive Behavior Analyzer) is a web application for behavioral data visualization, which provides a series of interactive visualizations, including the temporal occurrences of behavioral events, the number and direction of interactions between individuals, the behavioral transitions and their respective transitional frequencies, as well as the visual and algorithmic comparison of the latter across data sets. It can therefore be applied to visualize behavior across individuals, species, or contexts. Several filtering options (selection of behaviors and individuals) together with options to set node and edge properties (in the network drawings) allow for interactive customization of the output drawings, which can also be downloaded afterwards. TIBA accepts data outputs from popular logging software and is implemented in Python and JavaScript, with all current browsers supported. The web application and usage instructions are available at tiba.inf.uni-konstanz.de. The source code is publicly available on GitHub: github.com/LSI-UniKonstanz/tiba., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Kraus et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background . In the context of pharmacokinetic analyses, the segmentation method one uses has a large impact on the results obtained, thus the importance of transparency. Innovation . This paper introduces a graphical user interface (GUI), TRU-IMP, that analyzes time-activity curves and segmentations in dynamic nuclear medicine. This GUI fills a gap in the current technological tools available for the analysis of quantitative dynamic nuclear medicine image acquisitions. The GUI includes various techniques of segmentations, with possibilities to compute related uncertainties. Results . The GUI was tested on image acquisitions made on a dynamic nuclear medicine phantom. This allows the comparison of segmentations via their time-activity curves and the extracted pharmacokinetic parameters. Implications . The flexibility and user-friendliness allowed by the proposed interface make the analyses both easy to perform and adjustable to any specific case. This GUI permits researchers to better show and understand the reproducibility, precision, and accuracy of their work in quantitative dynamic nuclear medicine. Availability and Implementation . Source code freely available on GitHub:https://github.com/ArGilfea/TRU-IMPand location of the interface available from there. The GUI is fully compatible with iOS and Windows operating systems (not tested on Linux). A phantom acquisition is also available to test the GUI easily., (Creative Commons Attribution license.)

Background: Multiple sequence alignment (MSA) has proven extremely useful in computational biology, especially in inferring evolutionary relationships via phylogenetic analysis and providing insight into protein structure and function. An alternative to the standard MSA model is partial order alignment (POA), in which aligned sequences are represented as paths in a graph rather than rows in a matrix. While the POA model has proven useful in several applications (e.g. sequencing reads assembly and pangenome structure exploration), we lack efficient visualization tools that could highlight its advantages., Results: We propose Sequence Flow - a web application designed to address the above problem. Sequence Flow presents the POA as a Sankey diagram, a kind of graph visualisation typically used for graphs representing flowcharts. Sequence Flow enables interactive alignment exploration, including fragment selection, highlighting a selected group of sequences, modification of the position of graph nodes, structure simplification etc. After adjustment, the visualization can be saved as a high-quality graphic file. Thanks to the use of SanKEY.js - a JavaScript library for creating Sankey diagrams, designed specifically to visualize POAs, Sequence Flow provides satisfactory performance even with large alignments., Conclusions: We provide Sankey diagram-based POA visualization tools for both end users (Sequence Flow) and bioinformatic software developers (SanKEY.js). Sequence Flow webservice is available at https://sequenceflow.mimuw.edu.pl/ . The source code for SanKEY.js is available at https://github.com/Krzysiekzd/SanKEY.js and for Sequence Flow at https://github.com/Krzysiekzd/SequenceFlow ., (© 2024. The Author(s).)

Graph neural networks (GNNs) have proven to be effective tools for the rapid and accurate prediction of crystal properties. While most existing methods focus on enriching representations of crystal structures, they do not deeply explore the characteristics of crystal graphs and leverage their intrinsic information from a data science perspective. In this work, we propose the potential multiplex crystal graph neural network (PMCGNN) for crystal property prediction. Based on the characteristics of crystal graphs, we reconstruct the crystal graph into a multiplex graph that includes two views: a global crystal graph embodying infinite potentials and a local crystal graph capturing local atomic interactions. We employ graph transformers (GTs) and message passing neural networks (MPNNs) architectures to learn the atomic representations of these two perspectives. Specifically, we augment the GT by incorporating positional encodings and structural encodings from the local crystal graph. This approach promotes interaction between the two perspectives, enabling the model to learn both node positional and graph structural information from different viewpoints through an attention mechanism. As a result, it enhances the model's ability to learn crystal representations. We conduct comprehensive experiments on the JARVIS and the Materials Project data sets for evaluation. Results show that PMCGNN presents superior performance in 9 crystal prediction tasks while maintaining reasonable computational expense.

Background: Network meta-analysis is developed to compare all available treatments; therefore it enriches evidence for clinical decision-making, offering insights into treatment effectiveness and safety when faced with multiple options. However, the complexity and numerous treatment comparisons in network meta-analysis can challenge healthcare providers and patients. The purpose of this study aimed to introduce a graphic design to present complex rankings of multiple interventions comprehensively., Methods: Our team members developed a "beading plot" to summary probability of achieving the best treatment (P-best) and global metrics including surface under the cumulative ranking curve (SUCRA) and P-score. Implemented via the "rankinma" R package, this tool summarizes rankings across diverse outcomes in network meta-analyses, and the package received an official release on the Comprehensive R Archive Network (CRAN). It includes the `PlotBead()` function for generating beading plots, which represent treatment rankings among various outcomes., Results: Beading plot has been designed based on number line plot, which effectively displays collective metrics for each treatment across various outcomes. Order on the -axis is derived from ranking metrics like P-best, SUCRA, and P-score. Continuous lines represent outcomes, and color-coded beads signify treatments., Conclusion: The beading plot is a valuable graphic that intuitively displays treatment rankings across diverse outcomes, enhancing reader-friendliness and aiding decision-making in complex network evidence scenarios. While empowering clinicians and patients to identify optimal treatments, it should be used cautiously, alongside an assessment of the overall evidence certainty., (© 2024. The Author(s).)

Objective:  Graph databases for electronic health record (EHR) data have become a useful tool for clinical research in recent years, but there is a lack of published methods to transform relational databases to a graph database schema. We developed a graph model for the Observational Medical Outcomes Partnership (OMOP) common data model (CDM) that can be reused across research institutions., Methods:  We created and evaluated four models, representing two different strategies, for converting the standardized clinical and vocabulary tables of OMOP into a property graph model within the Neo4j graph database. Taking the Successful Clinical Response in Pneumonia Therapy (SCRIPT) and Collaborative Resource for Intensive care Translational science, Informatics, Comprehensive Analytics, and Learning (CRITICAL) cohorts as test datasets with different sizes, we compared two of the resulting graph models with respect to database performance including database building time, query complexity, and runtime for both cohorts., Results:  Utilizing a graph schema that was optimized for storing critical information as topology rather than attributes resulted in a significant improvement in both data creation and querying. The graph database for our larger cohort, CRITICAL, can be built within 1 hour for 134,145 patients, with a total of 749,011,396 nodes and 1,703,560,910 edges., Discussion:  To our knowledge, this is the first generalized solution to convert the OMOP CDM to a graph-optimized schema. Despite being developed for studies at a single institution, the modeling method can be applied to other OMOP CDM v5.x databases. Our evaluation with the SCRIPT and CRITICAL cohorts and comparison between the current and previous versions show advantages in code simplicity, database building, and query speed., Conclusion:  We developed a method for converting OMOP CDM databases into graph databases. Our experiments revealed that the final model outperformed the initial relational-to-graph transformation in both code simplicity and query efficiency, particularly for complex queries., Competing Interests: J.A.A.-G. is an employee of Neo4j. J.A.A.-G. joined the project after Neo4j was selected as our graph database engine and did not play a role in that decision. All other authors have no relevant conflicts to disclose., (Thieme. All rights reserved.)

A Virtual Reality Laboratory (VR Lab) experiment refers to an experiment session that is being conducted in the virtual environment through Virtual Reality (VR) and aims to deliver procedural knowledge to students similar to that in a physical lab environment. While VR Lab is becoming more popular among education institutes as a learning tool for students, existing designs are mostly considered from a student's perspective. Instructors could only receive limited information on how the students are performing and could not provide useful feedback to aid the students' learning and evaluate their performance. This motivated us to create VisTA-LIVE: a Visualization Tool for Assessment of Laboratories In Virtual Environments. In this article, we present in detail the design thinking approach that was applied to create VisTA-LIVE. The tool is deployed in an Extended Reality (XR) environment, and we report the evaluation results with domain experts and discuss issues related to monitoring and assessing a live VR lab session which lay potential directions for future work. We also describe how the resulting design of the tool could be used as a reference for other education developers who wish to develop similar applications.

In this study, we explored the impact of tilted designs of anthropomorphic app icons on users' perceptions of icon vividness across three experiments. In Experiment 1, tilting with an angle of 45° to the left increased perceived icon vividness. In Experiment 2, sequential icon tilt angles at 30° intervals manipulation showed that small tilt angles (e.g., 30° to the left or right) enhanced participant perceptions of dynamism and vividness, and participants perceived greater vividness in anthropomorphic app icons with slight tilting, driven by this increased dynamism. In Experiment 3, we excluded the effect of the completeness of icons on these participants' evaluations and affirmed that slightly tilting designs was an effective visual strategy for improving perceived vividness to attract users., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Augmented reality is one of the enabling technologies of the upcoming future. Its usage in working and learning scenarios may lead to a better quality of work and training by helping the operators during the most crucial stages of processes. Therefore, the automatic detection of stress during augmented reality experiences can be a valuable support to prevent consequences on people's health and foster the spreading of this technology. In this work, we present the design of a non-invasive stress assessment approach. The proposed system is based on the analysis of the head movements of people wearing a Head Mounted Display while performing stress-inducing tasks. First, we designed a subjective experiment consisting of two stress-related tests for data acquisition. Then, a statistical analysis of head movements has been performed to determine which features are representative of the presence of stress. Finally, a stress classifier based on a combination of Support Vector Machines has been designed and trained. The proposed approach achieved promising performances thus paving the way for further studies in this research direction.