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.

• MeSH
• mikroskopie MeSH
• počítačové zpracování obrazu MeSH
• průběh práce * MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Phosphorylation is one of the quickest post-translational modifications that controls downstream signaling pathways regulating processes like cell proliferation, survival, and differentiation. Nowadays, mass spectrometry-based phosphoproteomics is a well-established method providing unprecedented characterization and quantification of phosphorylated proteins and peptides in complex samples. A comprehensive phosphoproteomics workflow consists of protein digestion, phosphopeptide enrichment, sample fractionation, chromatographic separation, and final detection by mass spectrometry. Each of these stages provides its own contribution to overall data variability and should be optimized thoroughly. This review aims to provide an overview of current developments in individual steps of phosphoproteomics workflow with a special focus on applied analytical methods. Recent efforts in all experimental steps are discussed. Finally, possible future development in the field of (phospho)proteomics is proposed.

• Klíčová slova
• Mass spectrometry, Phosphoproteomics, Receptor tyrosine kinase, Signaling pathways, Workflow,
• MeSH
• analýza dat * MeSH
• fosfopeptidy analýza   MeSH
• fosfoproteiny analýza   MeSH
• fosforylace MeSH
• hmotnostní spektrometrie metody   MeSH
• proteomika * metody   MeSH
• průběh práce MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• fosfopeptidy MeSH
• fosfoproteiny MeSH

Recording the provenance of scientific computation results is key to the support of traceability, reproducibility and quality assessment of data products. Several data models have been explored to address this need, providing representations of workflow plans and their executions as well as means of packaging the resulting information for archiving and sharing. However, existing approaches tend to lack interoperable adoption across workflow management systems. In this work we present Workflow Run RO-Crate, an extension of RO-Crate (Research Object Crate) and Schema.org to capture the provenance of the execution of computational workflows at different levels of granularity and bundle together all their associated objects (inputs, outputs, code, etc.). The model is supported by a diverse, open community that runs regular meetings, discussing development, maintenance and adoption aspects. Workflow Run RO-Crate is already implemented by several workflow management systems, allowing interoperable comparisons between workflow runs from heterogeneous systems. We describe the model, its alignment to standards such as W3C PROV, and its implementation in six workflow systems. Finally, we illustrate the application of Workflow Run RO-Crate in two use cases of machine learning in the digital image analysis domain.

• MeSH
• průběh práce * MeSH
• reprodukovatelnost výsledků MeSH
• software MeSH
• strojové učení MeSH
• Publikační typ
• časopisecké články MeSH

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.

• Klíčová slova
• best practices, brain data, data lifecycle, health information system, health-related data, ontology, physical data, workflow,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Edge computing is a novel technology, which is closely related to the concept of Internet of Things. This technology brings computing resources closer to the location where they are consumed by end-users-to the edge of the cloud. In this way, response time is shortened and lower network bandwidth is utilized. Workflow scheduling must be addressed to accomplish these goals. In this paper, we propose an enhanced firefly algorithm adapted for tackling workflow scheduling challenges in a cloud-edge environment. Our proposed approach overcomes observed deficiencies of original firefly metaheuristics by incorporating genetic operators and quasi-reflection-based learning procedure. First, we have validated the proposed improved algorithm on 10 modern standard benchmark instances and compared its performance with original and other improved state-of-the-art metaheuristics. Secondly, we have performed simulations for a workflow scheduling problem with two objectives-cost and makespan. We performed comparative analysis with other state-of-the-art approaches that were tested under the same experimental conditions. Algorithm proposed in this paper exhibits significant enhancements over the original firefly algorithm and other outstanding metaheuristics in terms of convergence speed and results' quality. Based on the output of conducted simulations, the proposed improved firefly algorithm obtains prominent results and managed to establish improvement in solving workflow scheduling in cloud-edge by reducing makespan and cost compared to other approaches.

• Klíčová slova
• Edge computing, Firefly algorithm, Genetic operator, Quasi-reflection-based learning, Swarm intelligence, Workflow scheduling,
• Publikační typ
• časopisecké články MeSH

Cryo-electron tomography (cryo-ET) is a groundbreaking technology for 3D visualisation and analysis of biomolecules in the context of cellular structures. It allows structural investigations of single proteins as well as their spatial arrangements within the cell. Cryo-tomograms provide a snapshot of the complex, heterogeneous and transient subcellular environment. Due to the excellent structure preservation in amorphous ice, it is possible to study interactions and spatial relationships of proteins in their native state without interference caused by chemical fixatives or contrasting agents. With the introduction of focused ion beam (FIB) technology, the preparation of cellular samples for electron tomography has become much easier and faster. The latest generation of integrated FIB and scanning electron microscopy (SEM) instruments (dual beam microscopes), specifically designed for cryo-applications, provides advances in automation, imaging and the preparation of high-pressure frozen bulk samples using cryo-lift-out technology. In addition, correlative cryo-fluorescence microscopy provides cellular targeting information through integrated software and hardware interfaces. The rapid advances, based on the combination of correlative cryo-microscopy, cryo-FIB and cryo-ET, have already led to a wealth of new insights into cellular processes and provided new 3D image data of the cell. Here we introduce our recent developments within the cryo-tomography workflow, and we discuss the challenges that lie ahead. LAY DESCRIPTION: This article describes our recent developments for the cryo-electron tomography (cryo-ET) workflow. Cryo-ET offers superior structural preservation and provides 3D snapshots of the interior of vitrified cells at molecular resolution. Before a cellular sample can be imaged by cryo-ET, it must be made accessible for transmission electron microscopy. This is achieved by preparing a 200-300 nm thin cryo-lamella from the cellular sample using a cryo-focused ion beam (cryo-FIB) microscope. Cryo-correlative light and electron microscopy (cryo-CLEM) is used within the workflow to guide the cryo-lamella preparation to the cellular areas of interest. We cover a basic introduction of the cryo-ET workflow and show new developments for cryo-CLEM, which facilitate the connection between the cryo-light microscope and the cryo-FIB. Next, we present our progress in cryo-FIB software automation to streamline cryo-lamella preparation. In the final section we demonstrate how the cryo-FIB can be used for 3D imaging and how bulk-frozen cellular samples (obtained by high-pressure freezing) can be processed using the newly developed cryo-lift-out technology.

• Klíčová slova
• Cryo-CLEM, FIB/SEM tomography, cryo-ET, cryo-FIB, cryo-FIB/SEM, cryo-LM, cryo-electron, cryo-focused ion beam, cryo-lift-out, electron-tomography, focused ion beam, lift-out, tomography workflow,
• MeSH
• automatizace MeSH
• elektronová kryomikroskopie * MeSH
• mikroskopie elektronová rastrovací MeSH
• průběh práce MeSH
• tomografie elektronová * MeSH
• transmisní elektronová mikroskopie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem 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
• Názvy látek
• DNA MeSH

BACKGROUND: A novel QDOT MICRO (Biosense Webster, Inc., Irvine, CA) catheter with optimized temperature control and microelectrodes was designed to incorporate real-time temperature sensing with contact force detection and microelectrodes to streamline ablation workflow. The QDOT-MICRO feasibility study evaluated the workflow, performance, and safety of temperature-controlled catheter ablation in patients with symptomatic paroxysmal atrial fibrillation with conventional ablation setting. METHODS: This was a non-randomized, single-arm, first-in-human study. The primary outcome was pulmonary vein isolation (PVI), confirmed by entrance block after adenosine and/or isoproterenol challenge. Safety outcomes included incidences of early-onset primary adverse events (AEs) and serious adverse device effects (SADEs). Device performance was evaluated via physician survey. RESULTS: All evaluated patients (n = 42) displayed 100% PVI. Two primary AEs (4.8%) were reported: 1 pericarditis and 1 vascular pseudoaneurysm. An additional SADE of localized infection was reported in 1 patient. No stroke, patient deaths, or other unanticipated AEs were reported. Average power delivered was 32.1±4.1 W, with a mean temperature of 40.8°C±1.6°C. Mean procedure (including 20-minute wait), fluoroscopy, and radiofrequency application times were 129.8, 6.7, and 34.0 minutes, respectively. On device performance, physicians reported overall satisfactory performance with the new catheter, with highest scores for satisfaction and usefulness of the temperature indicator. CONCLUSIONS: Initial clinical experience with the novel catheter showed 100% acute PVI success and acceptable safety and device performance in temperature-controlled ablation mode. There were no deaths, stroke, or unanticipated AEs. Fluoroscopy and procedural times were short and similar or better than reported for prior generation catheters.

• Klíčová slova
• Arrhythmia, Atrial fibrillation, Catheter ablation, Pulmonary vein isolation, Workflow,
• Publikační typ
• časopisecké články 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.

• Klíčová slova
• CAD/CAM, bleaching, digital dentistry, operative dentistry, periodontics/orthodontics,
• 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
• Názvy látek
• složené pryskyřice MeSH

Macroautophagy is often quantified by live imaging of autophagosomes labeled with fluorescently tagged ATG8 protein (FP-ATG8) in Arabidopsis thaliana. The labeled particles are then counted in single focal planes. This approach may lead to inaccurate results as the actual 3D distribution of autophagosomes is not taken into account and appropriate sampling in the Z-direction is not performed. To overcome this issue, we developed a workflow consisting of immunolabeling of autophagosomes with an anti-ATG8 antibody followed by stereological image analysis using the optical disector and the Cavalieri principle. Our protocol specifically recognized autophagosomes in epidermal cells of Arabidopsis root. Since the anti-ATG8 antibody recognizes multiple AtATG8 isoforms, we were able to detect a higher number of immunolabeled autophagosomes than with the FP-AtATG8e marker, that most probably does not recognize all autophagosomes in a cell. The number of autophagosomes per tissue volume positively correlated with the intensity of autophagy induction. Compared with the quantification of autophagosomes in maximum intensity projections, stereological methods were able to detect the autophagosomes present in a given volume with higher accuracy. Our novel workflow provides a powerful toolkit for unbiased and reproducible quantification of autophagosomes and offers a convenient alternative to the standard of live imaging with FP-ATG8 markers.

• Klíčová slova
• ATG8, Cavalieri principle, autophagosome, autophagy, image analysis, immunofluorescence, immunolabeling, microscopy, optical disector, stereology,
• MeSH
• Arabidopsis * metabolismus   MeSH
• autofagie MeSH
• autofagozomy * metabolismus   MeSH
• kořeny rostlin * metabolismus   MeSH
• proteiny huseníčku metabolismus   MeSH
• průběh práce MeSH
• rodina proteinů Atg8 metabolismus   genetika   MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny huseníčku MeSH
• rodina proteinů Atg8 MeSH