Virtual Needle Insertion with Enhanced Haptic Feedback for Guidance and Needle-Tissue Interaction Forces.

Interventional radiologists mainly rely on visual feedback via imaging modalities to steer a needle toward a tumor during biopsy and ablation procedures. In the case of CT-guided procedures, there is a risk of exposure to hazardous X-ray-based ionizing radiation. Therefore, CT scans are usually not used continuously, which increases the chances of a misplacement of the needle and the need for reinsertion, leading to more tissue trauma. Interventionalists also encounter haptic feedback via needle-tissue interaction forces while steering a needle. These forces are useful but insufficient to clearly perceive and identify deep-tissue structures such as tumors. The objective of this paper was to investigate the effect of enhanced force feedback for sensing interaction forces and guiding the needle when applied individually and simultaneously during a virtual CT-guided needle insertion task. We also compared the enhanced haptic feedback to enhanced visual feedback. We hypothesized that enhancing the haptic feedback limits the time needed to reach the target accurately and reduces the number of CT scans, as the interventionalist depends more on real-time enhanced haptic feedback. To test the hypothesis, a simulation environment was developed to virtually steer a needle in five degrees of freedom (DoF) to reach a tumor target embedded in a liver model. Twelve participants performed in the experiment with different feedback conditions where we measured their performance in terms of the following: targeting accuracy, trajectory tracking, number of CT scans required, and the time needed to finish the task. The results suggest that the combination of enhanced haptic feedback for guidance and sensing needle-tissue interaction forces significantly reduce the number of scans and the duration required to finish the task by 32.1% and 46.9%, respectively, when compared to nonenhanced haptic feedback. The other feedback modalities significantly reduced the duration to finish the task by around 30% compared to nonenhanced haptic feedback.

Usability Evaluation Methods Used in Electronic Discharge Summaries: Literature Review.

BACKGROUND: With the widespread adoption of digital health records, including electronic discharge summaries (eDS), it is important to assess their usability in order to understand whether they meet the needs of the end users. While there are established approaches for evaluating the usability of electronic health records, there is a lack of knowledge regarding suitable evaluation methods specifically for eDS. OBJECTIVE: This literature review aims to identify the usability evaluation approaches used in eDS. METHODS: We conducted a comprehensive search of PubMed, CINAHL, Web of Science, ACM Digital Library, MEDLINE, and ProQuest databases from their inception until July 2023. The study information was extracted and reported in accordance with the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). We included studies that assessed the usability of eDS, and the systems used to display eDS. RESULTS: A total of 12 records, including 11 studies and 1 thesis, met the inclusion criteria. The included studies used qualitative, quantitative, or mixed methods approaches and reported the use of various usability evaluation methods. Heuristic evaluation was the most used method to assess the usability of eDS systems (n=7), followed by the think-aloud approach (n=5) and laboratory testing (n=3). These methods were used either individually or in combination with usability questionnaires (n=3) and qualitative semistructured interviews (n=4) for evaluating eDS usability issues. The evaluation processes incorporated usability metrics such as user performance, satisfaction, efficiency, and impact rating. CONCLUSIONS: There are a limited number of studies focusing on usability evaluations of eDS. The identified studies used expert-based and user-centered approaches, which can be used either individually or in combination to identify usability issues. However, further research is needed to determine the most appropriate evaluation method which can assess the fitness for purpose of discharge summaries.

Computational insights into inhibiting EphA2: Integrating structure-based virtual screening, docking, and molecular dynamics simulations for small molecule discovery.

Elevated expression and dysfunction of ephrin type A receptor-2 (EphA2) have been implicated in the initiation and progression of cancer, metastasis, and unfavorable clinical outcomes. A promising strategy to counteract this dysregulation involves the development of small-molecule inhibitors that target EphA2. Our study focuses on this objective. To initiate Structure-Based Virtual Screening (SBVS), we leveraged an advanced online platform, the Mcule database, which houses an extensive collection of millions of chemical compounds. Using drug similarity filters, we efficiently identified ten thousand potential hits. By further refining the selection through toxicity profiling, we prudently narrowed down the candidates to a more manageable set of 100 molecules. Using the Mcule Single Click, DockThor, and SwissDock tools, we conducted multi-scoring docking assessments of thirty-seven compounds that satisfied the ADME standards. A comprehensive evaluation of Gibbs binding free energy terms, as derived from these docking tools, facilitated the identification of top-ranking docking hits. Remarkably, among the known inhibitors, dasatinib displayed the most robust binding to EphA2 with an average ΔG of -9.0 kcal/mol. Intriguingly, alternatives have emerged in recent years. Notably, small molecules such as Mcule-1579910267 (ΔG: -9.3 kcal/mol), Mcule-1893218381 (ΔG: -9.2 kcal/mol), Mcule-3981378344 (ΔG: -9.3 kcal/mol), and Mcule-8617639093 (ΔG: -9.1 kcal/mol) exhibited a notably strong binding affinity to EphA2, rivaling dasatinib. Subsequently, the four leading ligands along with dasatinib were selected for the MD simulations. Our rigorous analyses during the MD simulation phase encompassing RMSD, RMSF, SASA, ΔGsolv, and Rg underscored the favorable stability of Mcule-8617639093. This compelling evidence ultimately signifies the potential for selective EphA2 inhibition.

Sense of embodiment with synchronized avatar during walking in mixed reality.

Gait guidance systems that synchronize the gait rhythm with an avatar in a mixed reality (MR) environment are attracting attention owing to their rehabilitation applications. More effective gait guidance can be achieved by changing body sensations for the sense of embodiment (SoE), which refers to the feeling of owning, controlling, and being inside a body in MR. This study investigated full-body synchronous motion between a human and a virtual avatar to enhance the SoE in walking with actual position changes in the real world. The full-body motion and gait rhythm were measured using body-worn inertial measurement units and a visual avatar was provided through a transparent head-mounted display. The results showed that the SoE of the participants was enhanced under higher synchronization conditions. In addition, questionnaire results showed that the SoE in the synchronous condition was significantly higher than that in the asynchronous condition, and the SoE in the self-avatar condition was significantly higher than that in the other-avatar condition. This indicates that a higher synchronization level with the appearance of an avatar leads to a stronger SoE in the human perception mechanism, which is important for potential application in medical or other fields.

Virtual modelling of the impact of torsional loading on osteoporotic vertebrae buckling.

Purpose: This study aimed to evaluate the biomechanical response or load transfer on the osteoporotic L1 vertebra under torsional loading. Methods: To achieve this goal, a numerical model of osteoporotic vertebra in various trabecular bone degenerations was developed and tested. The mechanical behavior of the model was represented taking into account the anisotropic properties of the cancellous bone, which provided a more realistic mechanical picture of the biological subsystem. To ensure the reliability of osteoporotic degradation, the thinning of cortical bone and the appearance of gaps between trabecular bone and cortical bone were also taken into account when creating the models. Results: Finite element (FE) analysis showed that the deformations of cortical bone thinning and detachment of the cortical bone from the trabecular tissue lead to local instability of the vertebra. As a result, the cortical bone of a vertebra loses its load-bearing capacity, even if the strength limit is not reached. Conclusions: The results obtained allow us to state that taking into account the thinning of the trabeculae, which creates voids, is extremely important for load-bearing capacity of osteoporotic vertebrae. However, a limitation of this study is the lack of experimental data to ensure consistency with the computer simulation results.

VCF observer: a user-friendly software tool for preliminary VCF file analysis and comparison.

BACKGROUND: Advancements over the past decade in DNA sequencing technology and computing power have created the potential to revolutionize medicine. There has been a marked increase in genetic data available, allowing for the advancement of areas such as personalized medicine. A crucial type of data in this context is genetic variant data which is stored in variant call format (VCF) files. However, the rapid growth in genomics has presented challenges in analyzing and comparing VCF files. RESULTS: In response to the limitations of existing tools, this paper introduces a novel web application that provides a user-friendly solution for VCF file analyses and comparisons. The software tool enables researchers and clinicians to perform high-level analysis with ease and enhances productivity. The application's interface allows users to conveniently upload, analyze, and visualize their VCF files using simple drag-and-drop and point-and-click operations. Essential visualizations such as Venn diagrams, clustergrams, and precision-recall plots are provided to users. A key feature of the application is its support for metadata-based file grouping, accomplished through flexible data matrix uploads, streamlining organization and analysis of user-defined categories. Additionally, the application facilitates standardized benchmarking of VCF files by integrating user-provided ground truth regions and variant lists. CONCLUSIONS: By providing a user-friendly interface and supporting essential visualizations, this software enhances the accessibility of VCF file analysis and assists researchers and clinicians in their scientific inquiries.

xiVIEW: Visualisation of Crosslinking Mass Spectrometry Data.

Crosslinking mass spectrometry (MS) has emerged as an important technique for elucidating the in-solution structures of protein complexes and the topology of protein-protein interaction networks. However, the expanding user community lacked an integrated visualisation tool that helped them make use of the crosslinking data for investigating biological mechanisms. We addressed this need by developing xiVIEW, a web-based application designed to streamline crosslinking MS data analysis, which we present here. xiVIEW provides a user-friendly interface for accessing coordinated views of mass spectrometric data, network visualisation, annotations extracted from trusted repositories like UniProtKB, and available 3D structures. In accordance with recent recommendations from the crosslinking MS community, xiVIEW (i) provides a standards compliant parser to improve data integration and (ii) offers accessible visualisation tools. By promoting the adoption of standard file formats and providing a comprehensive visualisation platform, xiVIEW empowers both experimentalists and modellers alike to pursue their respective research interests. We anticipate that xiVIEW will advance crosslinking MS-inspired research, and facilitate broader and more effective investigations into complex biological systems.

DockThor-VS: A Free Platform for Receptor-Ligand Virtual Screening.

The DockThor-VS platform (https://dockthor.lncc.br/v2/) is a free protein-ligand docking server conceptualized to facilitate and assist drug discovery projects to perform docking-based virtual screening experiments accurately and using high-performance computing. The DockThor docking engine is a grid-based method designed for flexible-ligand and rigid-receptor docking. It employs a multiple-solution genetic algorithm and the MMFF94S molecular force field scoring function for pose prediction. This engine was engineered to handle highly flexible ligands, such as peptides. Affinity prediction and ranking of protein-ligand complexes are performed with the linear empirical scoring function DockTScore. The main steps of the ligand and protein preparation are available on the DockThor Portal, making it possible to change the protonation states of the amino acid residues, and include cofactors as rigid entities. The user can also customize and visualize the main parameters of the grid box. The results of docking experiments are automatically clustered and ordered, providing users with a diverse array of meaningful binding modes. The platform DockThor-VS offers a user-friendly interface and powerful algorithms, enabling researchers to conduct virtual screening experiments efficiently and accurately. The DockThor Portal utilizes the computational strength of the Brazilian high-performance platform SDumont, further amplifying the efficiency and speed of docking experiments. Additionally, the web server facilitates and enhances virtual screening experiments by offering curated structures of potential targets and compound datasets, such as proteins related to COVID-19 and FDA-approved drugs for repurposing studies. In summary, DockThor-VS is a dynamic and evolving solution for docking-based virtual screening to be applied in drug discovery projects.

Usability, Ergonomics, and Educational Value of a Novel Telestration Tool for Surgical Coaching: Usability Study.

BACKGROUND: Telementoring studies found technical challenges in achieving accurate and stable annotations during live surgery using commercially available telestration software intraoperatively. To address the gap, a wireless handheld telestration device was developed to facilitate dynamic user interaction with live video streams. OBJECTIVE: This study aims to find the perceived usability, ergonomics, and educational value of a first-generation handheld wireless telestration platform. METHODS: A prototype was developed with four core hand-held functions: (1) free-hand annotation, (2) cursor navigation, (3) overlay and manipulation (rotation) of ghost (avatar) instrumentation, and (4) hand-held video feed navigation on a remote monitor. This device uses a proprietary augmented reality platform. Surgeons and trainees were invited to test the core functions of the platform by performing standardized tasks. Usability and ergonomics were evaluated with a validated system usability scale and a 5-point Likert scale survey, which also evaluated the perceived educational value of the device. RESULTS: In total, 10 people (9 surgeons and 1 senior resident; 5 male and 5 female) participated. Participants strongly agreed or agreed (SA/A) that it was easy to perform annotations (SA/A 9, 90% and neutral 0, 0%), video feed navigation (SA/A 8, 80% and neutral 1, 10%), and manipulation of ghost (avatar) instruments on the monitor (SA/A 6, 60% and neutral 3, 30%). Regarding ergonomics, 40% (4) of participants agreed or strongly agreed (neutral 4, 40%) that the device was physically comfortable to use and hold. These results are consistent with open-ended comments on the device's size and weight. The average system usability scale was 70 (SD 12.5; median 75, IQR 63-84) indicating an above average usability score. Participants responded favorably to the device's perceived educational value, particularly for postoperative coaching (agree 6, 60%, strongly agree 4, 40%). CONCLUSIONS: This study presents the preliminary usability results of a novel first-generation telestration tool customized for use in surgical coaching. Favorable usability and perceived educational value were reported. Future iterations of the device should focus on incorporating user feedback and additional studies should be conducted to evaluate its effectiveness for improving surgical education. Ultimately, such tools can be incorporated into pedagogical models of surgical coaching to optimize feedback and training.

Interactive tools for functional annotation of bacterial genomes.

Automated annotations of protein functions are error-prone because of our lack of knowledge of protein functions. For example, it is often impossible to predict the correct substrate for an enzyme or a transporter. Furthermore, much of the knowledge that we do have about the functions of proteins is missing from the underlying databases. We discuss how to use interactive tools to quickly find different kinds of information relevant to a protein's function. Many of these tools are available via PaperBLAST (http://papers.genomics.lbl.gov). Combining these tools often allows us to infer a protein's function. Ideally, accurate annotations would allow us to predict a bacterium's capabilities from its genome sequence, but in practice, this remains challenging. We describe interactive tools that infer potential capabilities from a genome sequence or that search a genome to find proteins that might perform a specific function of interest. Database URL: http://papers.genomics.lbl.gov.

MassLite: An integrated python platform for single cell mass spectrometry metabolomics data pretreatment with graphical user interface and advanced peak alignment method.

Mass spectrometry (MS) has been one of the most widely used tools for bioanalytical analysis due to its high sensitivity, capability of quantitative analysis, and compatibility with biomolecules. Among various MS techniques, single cell mass spectrometry (SCMS) is an advanced approach to molecular analysis of cellular contents in individual cells. In tandem with the creation of novel experimental techniques, the development of new SCMS data analysis tools is equally important. As most published software packages are not specifically designed for pretreatment of SCMS data, including peak alignment and background removal, their applicability on processing SCMS data is generally limited. Hereby we introduce a Python platform, MassLite, specifically designed for rapid SCMS metabolomics data pretreatment. This platform is made user-friendly with graphical user interface (GUI) and exports data in the forms of each individual cell for further analysis. A core function of this tool is to use a novel peak alignment method that avoids the intrinsic drawbacks of traditional binning method, allowing for more effective handling of MS data obtained from high resolution mass spectrometers. Other functions, such as void scan filtering, dynamic grouping, and advanced background removal, are also implemented in this tool to improve pretreatment efficiency.

CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation.

Molecular modeling and simulation serve an important role in exploring biological functions of proteins at the molecular level, which is complementary to experiments. CHARMM-GUI (https://www.charmm-gui.org) is a web-based graphical user interface that generates complex molecular simulation systems and input files, and we have been continuously developing and expanding its functionalities to facilitate various complex molecular modeling and make molecular dynamics simulations more accessible to the scientific community. Currently, covalent drug discovery emerges as a popular and important field. Covalent drug forms a chemical bond with specific residues on the target protein, and it has advantages in potency for its prolonged inhibition effects. Even though there are higher demands in modeling PDB protein structures with various covalent ligand types, proper modeling of covalent ligands remains challenging. This work presents a new functionality in CHARMM-GUI PDB Reader & Manipulator that can handle a diversity of ligand-amino acid linkage types, which is validated by a careful benchmark study using over 1,000 covalent ligand structures in RCSB PDB. We hope that this new functionality can boost the modeling and simulation study of covalent ligands.

Integration of Trusted Third Party Software into an EDC System for Data Protection - Compliant Identity Management, Consent Management and Pseudonymization in Medical Research Studies.

INTRODUCTION: Medical research studies which involve electronic data capture of sensitive data about human subjects need to manage medical and identifying participant data in a secure manner. To protect the identity of data subjects, an independent trusted third party should be responsible for pseudonymization and management of the identifying data. METHODS: We have developed a web-based integrated solution that combines REDCap as an electronic data capture system with the trusted third party software tools of the University Medicine Greifswald, which provides study personnel with a single user interface for both clinical data entry and management of identities, pseudonyms and informed consents. RESULTS: Integration of the two platforms enables a seamless workflow of registering new participants, entering identifying and consent information, and generating pseudonyms in the trusted third party system, with subsequent capturing of medical data in the electronic data capture system, while maintaining strict separation of medical and identifying data in the two independently managed systems. CONCLUSION: Our solution enables a time-efficient data entry workflow, provides a high level of data protection by minimizing visibility of identifying information and pseudonym lists, and avoids errors introduced by manual transfer of pseudonyms between separate systems.

Visualization Techniques for Summarizing Single Patient Health Data to Support Physicians' Clinical Decisions - A Scoping Review.

INTRODUCTION: User-centered data visualizations can reduce physician cognitive load and support clinical decision making. To facilitate the selection of appropriate visualizations for single patient health data summaries, this scoping review provides a literature overview of possible visualization techniques and the corresponding reported user-centered design phases. METHODS: The publication databases PubMed, Web of Science, IEEE Xplore and ACM Digital Library were searched for relevant articles from 2017 to 2022. RESULTS: Of the 777 articles screened, 78 articles were included in the final analysis. The most commonly used visualization techniques are table, scatterplot-line timeline, text and event timelines, with 24 other visualization techniques identified. The testing phase of the user centered design process is reported most frequently. CONCLUSION: This scoping review can support developers in the selection of suitable visualizations for single patient health data by revealing the design space of possible visualization techniques.

Designing an mHealth Application to Support Horse Owners in Assessing Their Horse's Health Status - Results of a Usability Test.

INTRODUCTION: Existing research agrees that a well-thought design of the user interface is a key point for an mHealth application for animal owners, supporting them obtain information and make decisions regarding their pet's specific situation. However, there is currently a lack of specific advice on the design of such an application. METHODS: As part of a user-centered design (UCD) process, a formative, explorative usability test with n = 5 users was conducted for collecting design ideas. The test was conducted for two applications that were already available on the market. RESULTS: The need of supporting comprehensive information input in guided processes that can be adapted to the individual level of knowledge, was identified as a key aspect. CONCLUSION: In this paper, recommendations for the design of a suitable user interface are suggested to support application developers and designers.

Digitalizing Handwritten Digits of Patients with Parkinson's Disease Utilizing Consumer Hardware and Open-Source Software.

INTRODUCTION: Parkinson's disease represents a burdensome condition with complex manifestations. A licensed, standardized paper-based questionnaire is completed by both patients and physicians to monitor the progression and state of the disease. However, integrating the obtained scores into digital systems still poses a challenge. METHODS: Paper-based handwriting is intuitive and an efficient mode of human-computer interaction. Accordingly, we transformed a consumer-grade tablet into a device where an exact digital copy of the disease-specific questionnaire can be filled with the supplied pen. Utilizing a small convolutional neural network directly on the device and trained on MNIST data, we translated the handwritten digits to appropriate LOINC codes and made them accessible through a FHIR-compatible HTTP interface. RESULTS: When evaluating the usability from a patient-centric point of view, the System Usability Score revealed an excellent rating (SUS = 83.01) from the participants. However, we identified some challenges associated with the magnetic pen and the flat design of the device. CONCLUSION: In setups where certified medical devices are not required, consumer hardware can be used to map handwritten digits of patients to appropriate medical standards without manual intervention through healthcare professionals.

[Virtual reality-brain computer interface hand function enhancement rehabilitation system incorporating multi-sensory stimulation].

Stroke is an acute cerebrovascular disease in which sudden interruption of blood supply to the brain or rupture of cerebral blood vessels cause damage to brain cells and consequently impair the patient's motor and cognitive abilities. A novel rehabilitation training model integrating brain-computer interface (BCI) and virtual reality (VR) not only promotes the functional activation of brain networks, but also provides immersive and interesting contextual feedback for patients. In this paper, we designed a hand rehabilitation training system integrating multi-sensory stimulation feedback, BCI and VR, which guides patients' motor imaginations through the tasks of the virtual scene, acquires patients' motor intentions, and then carries out human-computer interactions under the virtual scene. At the same time, haptic feedback is incorporated to further increase the patients' proprioceptive sensations, so as to realize the hand function rehabilitation training based on the multi-sensory stimulation feedback of vision, hearing, and haptic senses. In this study, we compared and analyzed the differences in power spectral density of different frequency bands within the EEG signal data before and after the incorporation of haptic feedback, and found that the motor brain area was significantly activated after the incorporation of haptic feedback, and the power spectral density of the motor brain area was significantly increased in the high gamma frequency band. The results of this study indicate that the rehabilitation training of patients with the VR-BCI hand function enhancement rehabilitation system incorporating multi-sensory stimulation can accelerate the two-way facilitation of sensory and motor conduction pathways, thus accelerating the rehabilitation process.

[Visual object detection system based on augmented reality and steady-state visual evoked potential].

This study investigates a brain-computer interface (BCI) system based on an augmented reality (AR) environment and steady-state visual evoked potentials (SSVEP). The system is designed to facilitate the selection of real-world objects through visual gaze in real-life scenarios. By integrating object detection technology and AR technology, the system augmented real objects with visual enhancements, providing users with visual stimuli that induced corresponding brain signals. SSVEP technology was then utilized to interpret these brain signals and identify the objects that users focused on. Additionally, an adaptive dynamic time-window-based filter bank canonical correlation analysis was employed to rapidly parse the subjects' brain signals. Experimental results indicated that the system could effectively recognize SSVEP signals, achieving an average accuracy rate of 90.6% in visual target identification. This system extends the application of SSVEP signals to real-life scenarios, demonstrating feasibility and efficacy in assisting individuals with mobility impairments and physical disabilities in object selection tasks.