Recent advancements in digital technologies have transformed clinical workflows in dentistry, ensuring precise restorations. Custom-made crowns and fixed partial dentures (FPDs) now rely on virtual articulation. The digital facebow provides individualized data for CAD settings, streamlining the fabrication via digital workflow. For the purpose of demonstrating the differences observed during fabrication, we present a case report involving a 68-year-old patient seeking a replacement for missing teeth 24, 25, 26, and 27. The treatment plan involved the fabrication of an implant-supported FPD using monolithic zirconia (ZrO2). However, technical hurdles emerged during the planning phase, primarily due to spatial limitations posing a risk of mechanical failure over time. Consequently, we pivoted approach towards a porcelain fused to metal (PFM) FPD. For the PFM FPD, individual values from the digital facebow adjusted both virtual and conventional articulators. For comparison, two ZrO2 FPDs were milled-individual settings and average settings. All restorations underwent assessment for occlusion in maximal intercuspal position and eccentric mandible movements. In conclusion, the case report showed that individualized PFM FPD required minimal adjustments compared to milled ZrO2 restorations, whether using individual or average values. Utilizing individual values from the digital facebow reduced operator working time and minimized the intraoral adjustments.
- MeSH
- Computer-Aided Design * MeSH
- Humans MeSH
- Workflow MeSH
- Aged MeSH
- Zirconium MeSH
- Crowns * MeSH
- Dental Prosthesis, Implant-Supported * methods MeSH
- Denture, Partial, Fixed MeSH
- Dental Prosthesis Design methods MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Aged MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
Pre-mRNA splicing represents an important regulatory layer of eukaryotic gene expression. In the simple budding yeast Saccharomyces cerevisiae, about one-third of all mRNA molecules undergo splicing, and splicing efficiency is tightly regulated, for example, during meiotic differentiation. S. cerevisiae features a streamlined, evolutionarily highly conserved splicing machinery and serves as a favourite model for studies of various aspects of splicing. RNA-seq represents a robust, versatile, and affordable technique for transcriptome interrogation, which can also be used to study splicing efficiency. However, convenient bioinformatics tools for the analysis of splicing efficiency from yeast RNA-seq data are lacking. We present a complete workflow for the calculation of genome-wide splicing efficiency in S. cerevisiae using strand-specific RNA-seq data. Our pipeline takes sequencing reads in the FASTQ format and provides splicing efficiency values for the 5' and 3' splice junctions of each intron. The pipeline is based on up-to-date open-source software tools and requires very limited input from the user. We provide all relevant scripts in a ready-to-use form. We demonstrate the functionality of the workflow using RNA-seq datasets from three spliceosome mutants. The workflow should prove useful for studies of yeast splicing mutants or of regulated splicing, for example, under specific growth conditions.
Direct composite restorations are accepted as a treatment option for microdontia, which is a relatively prevalent condition that poses esthetic concerns. While free-hand composite placement is technique-sensitive and time-consuming, the resin composite injection technique is more straightforward and predictable. A fully digital workflow has been recently introduced, but the 3D-printed resin index is rigid and challenged by undercuts, as opposed to the silicone index. This case report presents a flexible 3D-printed resin index, which can accurately transfer the digitally simulated functional and esthetic form to the final restoration. In addition, a rigid stabilization holder was designed to stabilize the flexible index.
- MeSH
- Printing, Three-Dimensional MeSH
- Esthetics, Dental * MeSH
- Humans MeSH
- Workflow MeSH
- Silicones MeSH
- Composite Resins * therapeutic use MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
SUMMARY: Here we introduce a Fiji plugin utilizing the HPC-as-a-Service concept, significantly mitigating the challenges life scientists face when delegating complex data-intensive processing workflows to HPC clusters. We demonstrate on a common Selective Plane Illumination Microscopy image processing task that execution of a Fiji workflow on a remote supercomputer leads to improved turnaround time despite the data transfer overhead. The plugin allows the end users to conveniently transfer image data to remote HPC resources, manage pipeline jobs and visualize processed results directly from the Fiji graphical user interface. AVAILABILITY AND IMPLEMENTATION: The code is distributed free and open source under the MIT license. Source code: https://github.com/fiji-hpc/hpc-workflow-manager/, documentation: https://imagej.net/SPIM_Workflow_Manager_For_HPC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Poor lifestyle leads potentially to chronic diseases and low-grade physical and mental fitness. However, ahead of time, we can measure and analyze multiple aspects of physical and mental health, such as body parameters, health risk factors, degrees of motivation, and the overall willingness to change the current lifestyle. In conjunction with data representing human brain activity, we can obtain and identify human health problems resulting from a long-term lifestyle more precisely and, where appropriate, improve the quality and length of human life. Currently, brain and physical health-related data are not commonly collected and evaluated together. However, doing that is supposed to be an interesting and viable concept, especially when followed by a more detailed definition and description of their whole processing lifecycle. Moreover, when best practices are used to store, annotate, analyze, and evaluate such data collections, the necessary infrastructure development and more intense cooperation among scientific teams and laboratories are facilitated. This approach also improves the reproducibility of experimental work. As a result, large collections of physical and brain health-related data could provide a robust basis for better interpretation of a person's overall health. This work aims to overview and reflect some best practices used within global communities to ensure the reproducibility of experiments, collected datasets and related workflows. These best practices concern, e.g., data lifecycle models, FAIR principles, and definitions and implementations of terminologies and ontologies. Then, an example of how an automated workflow system could be created to support the collection, annotation, storage, analysis, and publication of findings is shown. The Body in Numbers pilot system, also utilizing software engineering best practices, was developed to implement the concept of such an automated workflow system. It is unique just due to the combination of the processing and evaluation of physical and brain (electrophysiological) data. Its implementation is explored in greater detail, and opportunities to use the gained findings and results throughout various application domains are discussed.
- Publication type
- Journal Article MeSH
- Review MeSH
The COVID-19 epidemic has spread across the world within months and creates multiple challenges for healthcare providers. Patients with cardiovascular disease represent a vulnerable population when suffering from COVID-19. Most hospitals have been facing difficulties in the treatment of COVID-19 patients, and there is a need to minimise patient flow time so that staff health is less endangered, and more patients can be treated. This article shows how to use simulation techniques to prepare hospitals for a virus outbreak. The initial simulation of the current processes of the heart clinic first identified the bottlenecks. It confirmed that the current workflow is not optimal for COVID-19 patients; therefore, to reduce waiting time, three optimisation scenarios are proposed. In the best situation, the discrete-event simulation of the second scenario led to a 62.3% reduction in patient waiting time. This is one of the few studies that show how hospitals can use workflow modelling using timed coloured Petri nets to manage healthcare systems in practice. This technique would be valuable in these challenging times as the health of staff, and other patients are at risk from the nosocomial transmission.
- MeSH
- Betacoronavirus MeSH
- COVID-19 MeSH
- Cardiology organization & administration MeSH
- Coronavirus Infections * MeSH
- Humans MeSH
- Pandemics * MeSH
- Computer Simulation MeSH
- Workflow * MeSH
- SARS-CoV-2 MeSH
- Pneumonia, Viral * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
18F-FDG PET/MRI might be the diagnostic method of choice for Hodgkin lymphoma patients, as it combines significant metabolic information from PET with excellent soft-tissue contrast from MRI and avoids radiation exposure from CT. However, a major issue is longer examination times than for PET/CT, especially for younger children needing anesthesia. Thus, a targeted selection of suitable whole-body MRI sequences is important to optimize the PET/MRI workflow. Methods: The initial PET/MRI scans of 84 EuroNet-PHL-C2 study patients from 13 international PET centers were evaluated. In each available MRI sequence, 5 PET-positive lymph nodes were assessed. If extranodal involvement occurred, 2 splenic lesions, 2 skeletal lesions, and 2 lung lesions were also assessed. A detection rate was calculated dividing the number of visible, anatomically assignable, and measurable lesions in the respective MRI sequence by the total number of lesions. Results: Relaxation time-weighted (T2w) transverse sequences with fat saturation (fs) yielded the best result, with detection rates of 95% for nodal lesions, 62% for splenic lesions, 94% for skeletal lesions, and 83% for lung lesions, followed by T2w transverse sequences without fs (86%, 49%, 16%, and 59%, respectively) and longitudinal relaxation time-weighted contrast-enhanced transverse sequences with fs (74%, 35%, 57%, and 55%, respectively). Conclusion: T2w transverse sequences with fs yielded the highest detection rates and are well suited for accurate whole-body PET/MRI in lymphoma patients. There is no evidence to recommend the use of contrast agents.
- MeSH
- Whole Body Imaging methods MeSH
- Diffusion Magnetic Resonance Imaging methods MeSH
- Child MeSH
- Fluorodeoxyglucose F18 MeSH
- Hodgkin Disease * diagnostic imaging pathology MeSH
- Humans MeSH
- Magnetic Resonance Imaging methods MeSH
- Bone Diseases * MeSH
- Positron Emission Tomography Computed Tomography MeSH
- Positron-Emission Tomography methods MeSH
- Workflow MeSH
- Radiopharmaceuticals MeSH
- Neoplasm Staging MeSH
- Check Tag
- Child MeSH
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Background: The Human Cell Differentiation Molecules (HCDM) organizes Human Leukocyte Differentiation Antigen (HLDA) workshops to test and name clusters of antibodies that react with a specific antigen. These cluster of differentiation (CD) markers have provided the scientific community with validated antibody clones, consistent naming of targets and reproducible identification of leukocyte subsets. Still, quantitative CD marker expression profiles and benchmarking of reagents at the single-cell level are currently lacking. Objective: To develop a flow cytometric procedure for quantitative expression profiling of surface antigens on blood leukocyte subsets that is standardized across multiple research laboratories. Methods: A high content framework to evaluate the titration and reactivity of Phycoerythrin (PE)-conjugated monoclonal antibodies (mAbs) was created. Two flow cytometry panels were designed: an innate cell tube for granulocytes, dendritic cells, monocytes, NK cells and innate lymphoid cells (12-color) and an adaptive lymphocyte tube for naive and memory B and T cells, including TCRγδ+, regulatory-T and follicular helper T cells (11-color). The potential of these 2 panels was demonstrated via expression profiling of selected CD markers detected by PE-conjugated antibodies and evaluated using 561 nm excitation. Results: Using automated data annotation and dried backbone reagents, we reached a robust workflow amenable to processing hundreds of measurements in each experiment in a 96-well plate format. The immunophenotyping panels enabled discrimination of 27 leukocyte subsets and quantitative detection of the expression of PE-conjugated CD markers of interest that could quantify protein expression above 400 units of antibody binding capacity. Expression profiling of 4 selected CD markers (CD11b, CD31, CD38, CD40) showed high reproducibility across centers, as well as the capacity to benchmark unique clones directed toward the same CD3 antigen. Conclusion: We optimized a procedure for quantitative expression profiling of surface antigens on blood leukocyte subsets. The workflow, bioinformatics pipeline and optimized flow panels enable the following: 1) mapping the expression patterns of HLDA-approved mAb clones to CD markers; 2) benchmarking new antibody clones to established CD markers; 3) defining new clusters of differentiation in future HLDA workshops.
- MeSH
- Antigens, Surface * metabolism MeSH
- Killer Cells, Natural metabolism MeSH
- Antigens, CD metabolism MeSH
- Leukocytes MeSH
- Humans MeSH
- Antibodies, Monoclonal MeSH
- Immunity, Innate * MeSH
- Workflow MeSH
- Flow Cytometry methods MeSH
- Reference Standards MeSH
- Reproducibility of Results MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Applying technologies of additive manufacturing to the field of tissue engineering created a pioneering new approach to model complex cell systems artificially. Regarding its huge potential, bioprinting is still in its infancies and many questions are still unanswered. To address this issue, an extrusion-based bioprinting (EBB) process was used to deposit human embryonic kidney (HEK) cells in a defined pattern. It was shown that the bioprinted construct featured a high degree in viability reaching up to 77% 10 days after printing (DAP). This work displays a proof of principle for a controlled cell formation which shall later be applied to in vitro drug screening tests using various types of cells.
- MeSH
- Biocompatible Materials chemical synthesis isolation & purification therapeutic use MeSH
- Biomedical Technology MeSH
- Bioprinting * methods instrumentation MeSH
- Cell Culture Techniques MeSH
- Microscopy, Fluorescence MeSH
- Humans MeSH
- Organ Culture Techniques MeSH
- In Vitro Techniques MeSH
- Tissue Engineering * methods instrumentation MeSH
- Check Tag
- Humans MeSH
