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The volume of nucleic acid sequence data has exploded recently, amplifying the challenge of transforming data into meaningful information. Processing data can require an increasingly complex ecosystem of customized tools, which increases difficulty in communicating analyses in an understandable way yet is of sufficient detail to enable informed decisions or repeats. This can be of particular interest to institutions and companies communicating computations in a regulatory environment. BioCompute Objects (BCOs; an instance of pipeline documentation that conforms to the IEEE 2791-2020 standard) were developed as a standardized mechanism for analysis reporting. A suite of BCOs is presented, representing interconnected elements of a computation modeled after those that might be found in a regulatory submission but are shared publicly - in this case a pipeline designed to identify viral contaminants in biological manufacturing, such as for vaccines.
Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.
The increasing diffusion of data acquisition systems paves the way to traceability based process management and definition. In the clinical context, IHE formalizes the reference guidelines, periodically enhanced to reflect processes evolution. In this work we describe how we have modeled the phlebotomy process following the IHE references and best-practices to obtain a fully traceable workflow. The work has resulted in two new transactions for the IHE LBL profile, describing samples containers production and samples collection. The complete workflow has been implemented and successfully tested in real clinical environments. The traceability data acquired have then been studied using Process Mining techniques to compare the production model with idealized workflow and guide further developments.
- MeSH
- algoritmy MeSH
- chybná diagnóza prevence a kontrola MeSH
- data mining MeSH
- flebotomie * MeSH
- klinické laboratorní techniky MeSH
- laboratoře normy MeSH
- navrhování softwaru * MeSH
- nemocniční informační systémy MeSH
- organizační modely MeSH
- počítačová simulace * MeSH
- počítačové systémy MeSH
- průběh práce MeSH
- řízení kvality MeSH
- sběr dat MeSH
- zajištění kvality zdravotní péče MeSH
- Publikační typ
- práce podpořená grantem MeSH
The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines.
- MeSH
- analýza dat MeSH
- benchmarking * MeSH
- proteiny MeSH
- proteomika * MeSH
- průběh práce MeSH
- software MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem 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.
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
- design s pomocí počítače * MeSH
- lidé MeSH
- průběh práce MeSH
- senioři MeSH
- zirkonium MeSH
- zubní korunky * MeSH
- zubní náhrada ve spojení s implantáty * metody MeSH
- zubní náhrady částečné fixní MeSH
- zubní protéza - design metody MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
BACKGROUND: A growing number of crystal and NMR structures reveals a considerable structural polymorphism of DNA architecture going well beyond the usual image of a double helical molecule. DNA is highly variable with dinucleotide steps exhibiting a substantial flexibility in a sequence-dependent manner. An analysis of the conformational space of the DNA backbone and the enhancement of our understanding of the conformational dependencies in DNA are therefore important for full comprehension of DNA structural polymorphism. RESULTS: A detailed classification of local DNA conformations based on the technique of Fourier averaging was published in our previous work. However, this procedure requires a considerable amount of manual work. To overcome this limitation we developed an automatic classification method consisting of the combination of supervised and unsupervised approaches. A proposed workflow is composed of k-NN method followed by a non-hierarchical single-pass clustering algorithm. We applied this workflow to analyze 816 X-ray and 664 NMR DNA structures released till February 2013. We identified and annotated six new conformers, and we assigned four of these conformers to two structurally important DNA families: guanine quadruplexes and Holliday (four-way) junctions. We also compared populations of the assigned conformers in the dataset of X-ray and NMR structures. CONCLUSIONS: In the present work we developed a machine learning workflow for the automatic classification of dinucleotide conformations. Dinucleotides with unassigned conformations can be either classified into one of already known 24 classes or they can be flagged as unclassifiable. The proposed machine learning workflow permits identification of new classes among so far unclassifiable data, and we identified and annotated six new conformations in the X-ray structures released since our previous analysis. The results illustrate the utility of machine learning approaches in the classification of local DNA conformations.
- MeSH
- algoritmy MeSH
- DNA chemie MeSH
- G-kvadruplexy MeSH
- klasifikace metody MeSH
- konformace nukleové kyseliny MeSH
- krystalografie rentgenová MeSH
- nukleární magnetická rezonance biomolekulární MeSH
- průběh práce MeSH
- shluková analýza MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
OBJECTIVE: Restorative treatment of anterior teeth is often required as the final step of orthodontic therapy to optimize the esthetics and function. This case report presents a direct minimally invasive approach for post-orthodontic recontouring of anterior teeth using the composite injection technique with a digital workflow. CLINICAL CONSIDERATIONS: The extraction of central incisors with short roots was indicated to resolve maxillary anterior crowding. The gained space was closed with lateral incisors, and it was necessary to recontour them and canines to resemble central and lateral incisors, respectively. The restorations were digitally designed, and a transparent silicone index was fabricated from a 3D-printed cast of the digital wax-up. After lateral incisors and canines were bonded with a universal adhesive in the etch-and-rinse mode, a highly filled injectable composite resin was applied into the index. The restorative treatment was preceded by gingivectomy using an Er:YAG laser and home bleaching. CONCLUSIONS: In cases where more complex recontouring of anterior teeth is necessary, the composite injection technique could be a suitable alternative to indirect restorations, because it is straightforward, cost-effective, and does not require any preparation. The digital workflow simplified and expedited the treatment while contributing to its precision. CLINICAL SIGNIFICANCE: Post-orthodontic recontouring using direct composite restorations is well accepted by patients due to low cost and non-invasiveness. However, in complicated cases, the free-hand technique is time-consuming and technique-sensitive. The presented composite injection technique with a digital workflow significantly simplifies and expedites the composite placement while predictably enhancing the treatment outcome.
- MeSH
- estetika stomatologická MeSH
- lidé MeSH
- průběh práce * MeSH
- řezáky MeSH
- složené pryskyřice MeSH
- trvalá zubní náhrada * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
