Reliability and Influence on Decision Making of fully-automated vs. semi-automated Software Packages for Procedural Planning in TAVI.
Ontology highlight
ABSTRACT:
SUBMITTER: Meyer A
PROVIDER: S-EPMC7329903 | biostudies-literature | 2020 Jul
REPOSITORIES: biostudies-literature
Publications
Reliability and Influence on Decision Making of fully-automated vs. semi-automated Software Packages for Procedural Planning in TAVI.
Meyer Alexander A Kofler Markus M Montagner Matteo M Unbehaun Axel A Sündermann Simon S Buz Semih S Klein Christoph C Stamm Christof C Solowjowa Natalia N Emmert Maximilian Y MY Falk Volkmar V Kempfert Jörg J
Scientific reports 20200701 1
Precise procedural planning is crucial to achieve excellent results in patients undergoing Transcatheter aortic valve implantation (TAVI). The aim of this study was to compare the semi-automated 3mensio (3 m) software to the fully-automated HeartNavigator3 (HN) software. We randomly selected 100 patients from our in-house TAVI-registry and compared aortic annulus and perimeter as well as coronary distances between 3m-measurements and post-hoc HN-measurements. Finally, we retrospectively simulate ...[more]
Similar Datasets
Project description:Even with advanced inverse-planning techniques, radiation treatment plan opti-mization remains a very time-consuming task with great output variability, which prompted the development of more automated approaches. One commercially available technique mimics the actions of experienced human operators to pro-gressively guide the traditional optimization process with automatically created regions of interest and associated dose-volume objectives. We report on the initial evaluation of this algorithm on 10 challenging cases of locoreginally advanced head and neck cancer. All patients were treated with VMAT to 70 Gy to the gross disease and 56 Gy to the elective bilateral nodes. The results of post-treatment autoplanning (AP) were compared to the original human-driven plans (HDP). We used an objective scoring system based on defining a collection of specific dosimetric metrics and corresponding numeric score functions for each. Five AP techniques with different input dose goals were applied to all patients. The best of them averaged the composite score 8% lower than the HDP, across the patient population. The difference in median values was statistically significant at the 95% confidence level (Wilcoxon paired signed-rank test p = 0.027). This result reflects the premium the institution places on dose homogeneity, which was consistently higher with the HDPs. The OAR sparing was consistently better with the APs, the differences reaching statistical significance for the mean doses to the parotid glands (p < 0.001) and the inferior pharyngeal constrictor (p = 0.016), as well as for the maximum doses to the spinal cord (p = 0.018) and brainstem (p = 0.040). If one is prepared to accept less stringent dose homogeneity criteria from the RTOG 1016 protocol, nine APs would comply with the protocol, while providing lower OAR doses than the HDPs. Overall, AP is a promising clinical tool, but it could benefit from a better process for shifting the balance between the target dose coverage/homogeneity and OAR sparing.
| S-EPMC5690942 | biostudies-literature
Project description:In this paper, we present a framework for automated shape differentiation in the finite element software NGSolve. Our approach combines the mathematical Lagrangian approach for differentiating PDE-constrained shape functions with the automated differentiation capabilities of NGSolve. The user can decide which degree of automatisation is required, thus allowing for either a more custom-like or black-box–like behaviour of the software. We discuss the automatic generation of first- and second-order shape derivatives for unconstrained model problems as well as for more realistic problems that are constrained by different types of partial differential equations. We consider linear as well as nonlinear problems and also problems which are posed on surfaces. In numerical experiments, we verify the accuracy of the computed derivatives via a Taylor test. Finally, we present first- and second-order shape optimisation algorithms and illustrate them for several numerical optimisation examples ranging from nonlinear elasticity to Maxwell’s equations. Supplementary Information The online version contains supplementary material available at 10.1007/s00158-020-02742-w.
| S-EPMC8550642 | biostudies-literature
Project description:The challenging complexity of biological structures has led to the development of several methods for quantitative analyses of form. Bones are shaped by the interaction of historical (phylogenetic), structural, and functional constrains. Consequently, bone shape has been investigated intensively in an evolutionary context. Geometric morphometric approaches allow the description of the shape of an object in all of its biological complexity. However, when biological objects present only few anatomical landmarks, sliding semi-landmarks may provide good descriptors of shape. The sliding procedure, mandatory for sliding semi-landmarks, requires several steps that may be time-consuming. We here compare the time required by two different software packages ('Edgewarp' and 'Morpho') for the same sliding task, and investigate potential differences in the results and biological interpretation. 'Morpho' is much faster than 'Edgewarp,' notably as a result of the greater computational power of the 'Morpho' software routines and the complexity of the 'Edgewarp' workflow. Morphospaces obtained using both software packages are similar and provide a consistent description of the biological variability. The principal differences between the two software packages are observed in areas characterized by abrupt changes in the bone topography. In summary, both software packages perform equally well in terms of the description of biological structures, yet differ in the simplicity of the workflow and time needed to perform the analyses.
| S-EPMC4655098 | biostudies-literature
Project description:PurposeTo propose and validate a fully automated multicriterial treatment planning solution for a CyberKnife® equipped with an InCiseTM 2 multileaf collimator.MethodsThe AUTO BAO plans are generated using fully automated prioritized multicriterial optimization (AUTO MCO) of pencil-beam fluence maps with integrated noncoplanar beam angle optimization (BAO), followed by MLC segment generation. Both the AUTO MCO and segmentation algorithms have been developed in-house. AUTO MCO generates for each patient a single, high-quality Pareto-optimal IMRT plan. The segmentation algorithm then accurately mimics the AUTO MCO 3D dose distribution, while considering all candidate beams simultaneously, rather than replicating the fluence maps. Pencil-beams, segment dose depositions, and final dose calculations are performed with a stand-alone version of the clinical dose calculation engine. For validation, AUTO BAO plans were generated for 33 prostate SBRT patients and compared to reference plans (REF) that were manually generated with the commercial treatment planning system (TPS), in absence of time pressure. REF plans were also compared to AUTO RB plans, for which fluence map optimization was performed for the beam angle configuration used in the REF plan, and the segmentation could use all these beams or only a subset, depending on the dosimetry.ResultsAUTO BAO plans were clinically acceptable and dosimetrically similar to REF plans, but had on average reduced numbers of beams ((beams in AUTO BAO)/(beams in REF) (relative improvement): 24.7/48.3 (-49%)), segments (59.5/98.9 (-40%)), and delivery times (17.1/22.3 min. (-23%)). Dosimetry of AUTO RB and REF were also similar, but AUTO RB used on average fewer beams (38.0/48.3 (-21%)) and had on average shorter delivery times (18.6/22.3 min. (-17%)). Delivered Monitor Units (MU) were similar for all three planning approaches.ConclusionsA new, vendor-independent optimization workflow for fully automated generation of deliverable high-quality CyberKnife® plans was proposed, including BAO. Compared to manual planning with the commercial TPS, fraction delivery times were reduced by 5.3 min. (-23%) due to large reductions in beam and segment numbers.
| S-EPMC8457110 | biostudies-literature
Project description:Purpose: Foxp2 is the first and for now the only gene connected to speech and language in humans. Two aminoacid substitutions took place in this protein during recent human evolution, after our split from the last common ancestor with chimpanzees, and are most likely to have undergone positive selection in human lineage (Enard et al., 2002). Methods: Transgenic mice in which the wild-type (murine) version of Foxp2 was replaced with the one bearing two human-specific amino acid substitutions (i.e. "humanized" Foxp2) - Foxp2hum/hum, have been compared to their wild-type (WT) counterparts in terms of behavior, electrophysiology and striatal gene expression. The latter was analyzed through RNA-sequencing performed on pooled indexed libraries on three flow cells on Illumina GAIIx. The reads were mapped to mouse genome (mm9) by TopHat 1.4.1 and were counted using Bedtools. mRNA profiles were obtained with more than 20 million reads for every sample. Differential gene expression was analyzed with DESeq using multifactor model (Anders and Huber, 2010). Results: Wild-type and Foxp2hum/hum mice did not show any significant differences in expression at individual gene level, neither in dorsomedial nor in dorsolateral striatum. However, when genes were grouped into functional categories and analyzed accordingly, this revealed a significant downregulation of functional categories related to synaptic signalling and plasticity in dorsomedial striatum of Foxp2hum/hum mice.
2014-09-24 | GSE60659 | GEO
Project description:Using primary cell culture to screen for changes in neuronal morphology requires specialized analysis software. We developed NeuronMetrics for semi-automated, quantitative analysis of two-dimensional (2D) images of fluorescently labeled cultured neurons. It skeletonizes the neuron image using two complementary image-processing techniques, capturing fine terminal neurites with high fidelity. An algorithm was devised to span wide gaps in the skeleton. NeuronMetrics uses a novel strategy based on geometric features called faces to extract a branch number estimate from complex arbors with numerous neurite-to-neurite contacts, without creating a precise, contact-free representation of the neurite arbor. It estimates total neurite length, branch number, primary neurite number, territory (the area of the convex polygon bounding the skeleton and cell body), and Polarity Index (a measure of neuronal polarity). These parameters provide fundamental information about the size and shape of neurite arbors, which are critical factors for neuronal function. NeuronMetrics streamlines optional manual tasks such as removing noise, isolating the largest primary neurite, and correcting length for self-fasciculating neurites. Numeric data are output in a single text file, readily imported into other applications for further analysis. Written as modules for ImageJ, NeuronMetrics provides practical analysis tools that are easy to use and support batch processing. Depending on the need for manual intervention, processing time for a batch of approximately 60 2D images is 1.0-2.5 h, from a folder of images to a table of numeric data. NeuronMetrics' output accelerates the quantitative detection of mutations and chemical compounds that alter neurite morphology in vitro, and will contribute to the use of cultured neurons for drug discovery.
| S-EPMC1945162 | biostudies-literature
Project description:PurposeTo determine whether the semi-automated two-dimensional echocardiography (2DE) layer strain software, compared to cardiac magnetic resonance (CMR), is reliable for left ventricular (LV) volume quantification.Methods and resultsWe retrospectively selected 84 patients who underwent CMR and 2DE on the same day. Novel 2DE layer strain software automatically provides LV contour in 3 myocardial layers and performs layer specific speckle tracking analysis, which calculates LV volumes, ejection fraction (LVEF), and global longitudinal strain (GLS) in each layer. These values were compared with reference values from CMR disk-area summation and feature tracking methods. Coverage probability (CP) was determined using predefined cut-off values and absolute differences in LV volumes of 30 mL, those in LVEF of 10%, and those in GLS of 4%. The software did not work in 3 patients (feasibility: 96%). Different layers resulted in different degrees of under- or over-estimation of LV volumes. Epicardial tracking significantly overestimated the LV volumes and significantly underestimated LVEF and GLS. Mid-myocardial tracking had less underestimation of LV volumes and equivalent CP values of LVEF (0.77 vs. 0.75 using the disk-area summation method and 0.90 vs. 0.94 using the feature tracking method) and GLS (0.95 vs. 0.92) compared with endocardial tracking. The new software showed excellent reproducibility, especially endocardial and mid-myocardial tracking.ConclusionsMid-myocardial tracking with the novel 2DE strain software provided less bias of LV volumes with high CP values of LVEF and GLS, which suggests that mid-myocardial layer speckle tracking analysis approximates CMR derived LV functional parameters.
| S-EPMC6716624 | biostudies-literature
Project description:Microbiome profiling holds great promise for the development of novel disease biomarkers and therapeutics. Next-generation sequencing is currently the preferred method for microbiome data collection and multiple standardized tools, packages, and pipelines have been developed for the purpose of raw data processing and microbial annotation. However, these currently available pipelines come with entry-level barriers such as high-performance hardware, software installation, and sequential command-line scripting that often deter end-users. We thus created Cloud Computing for Microbiome Profiling (CCMP, https://ccmp.usc.edu), a public cloud-based web tool which combines the analytical power of current microbiome analysis platforms with a user-friendly interface. CCMP is a free-of-charge software-as-a-service (SaaS) that simplifies user experience by enabling users to complete their analysis in a single step, uploading raw sequencing data files. Once users upload 16S ribosomal RNA gene sequence data, our pipeline performs taxonomic annotation, abundance profiling, and statistical tests to report microbiota signatures altered by diseases or experimental conditions. CCMP took a 125 gigabyte (GB) input of 16S ribosomal RNA gene sequence data from 1052 specimens in FASTQ format and reported figures and tables of taxonomic annotations, statistical tests, ? and ? diversity calculations, and principal coordinate analyses within 21 hours. CCMP is the first fully-automated web interface that integrates three key solutions for large-scale data analysis: cloud computing, fast file transfer technology, and microbiome analysis tools. As a reliable platform that supplies consistent microbiome analysis, CCMP will advance microbiome research by making effortful bioinformatics easily accessible to public.
| S-EPMC6719681 | biostudies-literature
Project description:BackgroundRelationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century.ResultsTreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves.ConclusionsDespite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.
| S-EPMC3111373 | biostudies-literature
Project description:Purpose: Foxp2 is the first and for now the only gene connected to speech and language in humans. Two aminoacid substitutions took place in this protein during recent human evolution, after our split from the last common ancestor with chimpanzees, and are most likely to have undergone positive selection in human lineage (Enard et al., 2002). Methods: Transgenic mice in which the wild-type (murine) version of Foxp2 was replaced with the one bearing two human-specific amino acid substitutions (i.e. "humanized" Foxp2) - Foxp2hum/hum, have been compared to their wild-type (WT) counterparts in terms of behavior, electrophysiology and striatal gene expression. The latter was analyzed through RNA-sequencing performed on pooled indexed libraries on three flow cells on Illumina GAIIx. The reads were mapped to mouse genome (mm9) by TopHat 1.4.1 and were counted using Bedtools. mRNA profiles were obtained with more than 20 million reads for every sample. Differential gene expression was analyzed with DESeq using multifactor model (Anders and Huber, 2010). Results: Wild-type and Foxp2hum/hum mice did not show any significant differences in expression at individual gene level, neither in dorsomedial nor in dorsolateral striatum. However, when genes were grouped into functional categories and analyzed accordingly, this revealed a significant downregulation of functional categories related to synaptic signalling and plasticity in dorsomedial striatum of Foxp2hum/hum mice. RNA-sequencing was performed on dorsomedial and dorsolateral striatum of wild-type and Foxp2hum/hum mice, on three flow cells Illumina GAIIx. The libraries from each sample were indexed and pooled together.
2014-09-24 | E-GEOD-60659 | biostudies-arrayexpress