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Baum D, Rolle A, Koschel D, Rostock L, Decker R, Sombati M, Öhme F, Plönes T. Long-Term Follow-Up after Laser-Assisted Pulmonary Metastasectomy Shows Complete Lung Function Recovery. Cancers (Basel) 2024; 16:1762. [PMID: 38730714 PMCID: PMC11083535 DOI: 10.3390/cancers16091762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Preserving maximum lung function is a fundamental goal of parenchymal-sparing pulmonary laser surgery. Long-term studies for follow-up of lung function after pulmonary laser metastasectomy are lacking. However, a sufficient postoperative lung function is essential for quality of life and reduces potential postoperative complications. In this study, we investigate the extent of loss in lung function following pulmonary laser resection after three, six, and twelve months. We conducted a retrospective analysis using a prospective database of 4595 patients, focusing on 126 patients who underwent unilateral pulmonary laser resection for lung metastases from 1996 to 2022 using a 1318 nm Nd:YAG laser or a high-power pure diode laser. Results show that from these patients, a median of three pulmonary nodules were removed, with 75% presenting central lung lesions and 25% peripheral lesions. The median preoperative FEV1 was 98% of the predicted value, decreasing to 71% postoperatively but improving to 90% after three months, 93% after six months, and 96% after twelve months. Statistical analysis using the Friedman test indicated no significant difference in FEV1 between preoperative levels and those at six and twelve months post-surgery. The findings confirm that pulmonary laser surgery effectively preserves lung function over time, with patients generally regaining their preoperative lung function within a year, regardless of the metastases' location.
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Affiliation(s)
- Daniel Baum
- Department of Thoracic Surgery, Fachkrankenhaus Coswig, Lung Center, Neucoswiger Str. 21, 01640 Coswig, Germany
| | - Axel Rolle
- Department of Thoracic Surgery, Fachkrankenhaus Coswig, Lung Center, Neucoswiger Str. 21, 01640 Coswig, Germany
| | - Dirk Koschel
- Division of Pneumology, Medical Department I, Medical Faculty and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany
- Department of Internal Medicine and Pneumology, Fachkrankenhaus Coswig, Lung Center, Neucoswiger Str. 21, 01640 Coswig, Germany
| | - Lysann Rostock
- Department of Thoracic Surgery, Fachkrankenhaus Coswig, Lung Center, Neucoswiger Str. 21, 01640 Coswig, Germany
| | - Rahel Decker
- Department of Thoracic Surgery, Fachkrankenhaus Coswig, Lung Center, Neucoswiger Str. 21, 01640 Coswig, Germany
- Division of Thoracic Surgery, Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC Dresden), Fetscherstraße 74, 01307 Dresden, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Medical Faculty and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, 01069 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
| | - Monika Sombati
- Department of Thoracic Surgery, Fachkrankenhaus Coswig, Lung Center, Neucoswiger Str. 21, 01640 Coswig, Germany
| | - Florian Öhme
- National Center for Tumor Diseases (NCT/UCC Dresden), Fetscherstraße 74, 01307 Dresden, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Medical Faculty and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, 01069 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- Division of Visceral Surgery, Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany
| | - Till Plönes
- Department of Thoracic Surgery, Fachkrankenhaus Coswig, Lung Center, Neucoswiger Str. 21, 01640 Coswig, Germany
- Division of Thoracic Surgery, Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany
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Klenert N, Lepper V, Baum D. A Local Iterative Approach for the Extraction of 2D Manifolds from Strongly Curved and Folded Thin-Layer Structures. IEEE Trans Vis Comput Graph 2024; 30:1260-1270. [PMID: 37930919 DOI: 10.1109/tvcg.2023.3327403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Ridge surfaces represent important features for the analysis of 3-dimensional (3D) datasets in diverse applications and are often derived from varying underlying data including flow fields, geological fault data, and point data, but they can also be present in the original scalar images acquired using a plethora of imaging techniques. Our work is motivated by the analysis of image data acquired using micro-computed tomography ([Formula: see text]) of ancient, rolled and folded thin-layer structures such as papyrus, parchment, and paper as well as silver and lead sheets. From these documents we know that they are 2-dimensional (2D) in nature. Hence, we are particularly interested in reconstructing 2D manifolds that approximate the document's structure. The image data from which we want to reconstruct the 2D manifolds are often very noisy and represent folded, densely-layered structures with many artifacts, such as ruptures or layer splitting and merging. Previous ridge-surface extraction methods fail to extract the desired 2D manifold for such challenging data. We have therefore developed a novel method to extract 2D manifolds. The proposed method uses a local fast marching scheme in combination with a separation of the region covered by fast marching into two sub-regions. The 2D manifold of interest is then extracted as the surface separating the two sub-regions. The local scheme can be applied for both automatic propagation as well as interactive analysis. We demonstrate the applicability and robustness of our method on both artificial data as well as real-world data including folded silver and papyrus sheets.
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Longren LL, Eigen L, Shubitidze A, Lieschnegg O, Baum D, Nyakatura JA, Hildebrandt T, Brecht M. Dense reconstruction of elephant trunk musculature. Curr Biol 2023; 33:4713-4720.e3. [PMID: 37757829 DOI: 10.1016/j.cub.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/15/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023]
Abstract
The elephant trunk operates as a muscular hydrostat1,2 and is actuated by the most complex musculature known in animals.3,4 Because the number of trunk muscles is unclear,5 we performed dense reconstructions of trunk muscle fascicles, elementary muscle units, from microCT scans of an Asian baby elephant trunk. Muscle architecture changes markedly across the trunk. Trunk tip and finger consist of about 8,000 extraordinarily filigree fascicles. The dexterous finger consists exclusively of microscopic radial fascicles pointing to a role of muscle miniaturization in elephant dexterity. Radial fascicles also predominate (at 82% volume) the remainder of the trunk tip, and we wonder if radial muscle fascicles are of particular significance for fine motor control of the dexterous trunk tip. By volume, trunk-shaft muscles6 comprise one-third of the numerous, small radial muscle fascicles; two-thirds of the three subtypes of large longitudinal fascicles (dorsal longitudinals, ventral outer obliques, and ventral inner obliques);7,8,9 and a small fraction of transversal fascicles. Shaft musculature is laterally, but not radially, symmetric. A predominance of dorsal over ventral radial muscles and of ventral over dorsal longitudinal muscles may result in a larger ability of the shaft to extend dorsally than ventrally10 and to bend inward rather than outward. There are around 90,000 trunk muscle fascicles. While primate hand control is based on fine control of contraction by the convergence of many motor neurons on a small set of relatively large muscles, evolution of elephant grasping has led to thousands of microscopic fascicles, which probably outnumber facial motor neurons.
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Affiliation(s)
- Luke L Longren
- Bernstein Center for Computational Neuroscience Berlin, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 6, 10115 Berlin, Germany; Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Lennart Eigen
- Bernstein Center for Computational Neuroscience Berlin, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 6, 10115 Berlin, Germany
| | - Ani Shubitidze
- Bernstein Center for Computational Neuroscience Berlin, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 6, 10115 Berlin, Germany
| | - Oliver Lieschnegg
- Bernstein Center for Computational Neuroscience Berlin, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 6, 10115 Berlin, Germany
| | - Daniel Baum
- Zuse-Institut Berlin, Takustraße 7, 14195 Berlin, Germany
| | - John A Nyakatura
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Thomas Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Michael Brecht
- Bernstein Center for Computational Neuroscience Berlin, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 6, 10115 Berlin, Germany; NeuroCure Cluster of Excellence, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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Kiewisz R, Baum D, Müller-Reichert T, Fabig G. Serial-section Electron Tomography and Quantitative Analysis of Microtubule Organization in 3D-reconstructed Mitotic Spindles. Bio Protoc 2023; 13:e4849. [PMID: 37900106 PMCID: PMC10603263 DOI: 10.21769/bioprotoc.4849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 10/31/2023] Open
Abstract
For the analysis of cellular architecture during mitosis, nanometer resolution is needed to visualize the organization of microtubules in spindles. Here, we present a detailed protocol that can be used to produce 3D reconstructions of whole mitotic spindles in cells grown in culture. For this, we attach mammalian cells enriched in mitotic stages to sapphire discs. Our protocol further involves cryo-immobilization by high-pressure freezing, freeze-substitution, and resin embedding. We then use fluorescence light microscopy to stage select mitotic cells in the resin-embedded samples. This is followed by large-scale electron tomography to reconstruct the selected and staged mitotic spindles in 3D. The generated and stitched electron tomograms are then used to semi-automatically segment the microtubules for subsequent quantitative analysis of spindle organization. Thus, by providing a detailed correlative light and electron microscopy (CLEM) approach, we give cell biologists a toolset to streamline the 3D visualization and analysis of spindle microtubules (http://kiewisz.shinyapps.io/asga). In addition, we refer to a recently launched platform that allows for an interactive display of the 3D-reconstructed mitotic spindles (https://cfci.shinyapps.io/ASGA_3DViewer/). Key features • High-throughput screening of mitotic cells by correlative light and electron microscopy (CLEM). • Serial-section electron tomography of selected cells. • Visualization of mitotic spindles in 3D and quantitative analysis of microtubule organization.
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Affiliation(s)
- Robert Kiewisz
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
- Experimental Center, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Biocomputing Unit, Centro Nacional de Biotechnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, Cantoblanco, Madrid, Spain
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Thomas Müller-Reichert
- Experimental Center, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gunar Fabig
- Experimental Center, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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Boelts J, Harth P, Gao R, Udvary D, Yáñez F, Baum D, Hege HC, Oberlaender M, Macke JH. Simulation-based inference for efficient identification of generative models in computational connectomics. PLoS Comput Biol 2023; 19:e1011406. [PMID: 37738260 PMCID: PMC10550169 DOI: 10.1371/journal.pcbi.1011406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 10/04/2023] [Accepted: 08/01/2023] [Indexed: 09/24/2023] Open
Abstract
Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neuronal networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters, and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a fixed wiring rule to fit the empirical data, SBI considers many parametrizations of a rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rule parameters and relies on machine learning methods to estimate a probability distribution (the 'posterior distribution over parameters conditioned on the data') that characterizes all data-compatible parameters. We demonstrate how to apply SBI in computational connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data.
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Affiliation(s)
- Jan Boelts
- Machine Learning in Science, University of Tübingen, Tübingen, Germany
- Tübingen AI Center, University of Tübingen, Tübingen, Germany
| | - Philipp Harth
- Department of Visual and Data-centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Richard Gao
- Machine Learning in Science, University of Tübingen, Tübingen, Germany
- Tübingen AI Center, University of Tübingen, Tübingen, Germany
| | - Daniel Udvary
- In Silico Brain Sciences, Max Planck Institute for Neurobiology of Behavior – caesar, Bonn, Germany
| | - Felipe Yáñez
- In Silico Brain Sciences, Max Planck Institute for Neurobiology of Behavior – caesar, Bonn, Germany
| | - Daniel Baum
- Department of Visual and Data-centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Hans-Christian Hege
- Department of Visual and Data-centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Marcel Oberlaender
- In Silico Brain Sciences, Max Planck Institute for Neurobiology of Behavior – caesar, Bonn, Germany
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Free University Amsterdam, Amsterdam, Netherlands
| | - Jakob H. Macke
- Machine Learning in Science, University of Tübingen, Tübingen, Germany
- Tübingen AI Center, University of Tübingen, Tübingen, Germany
- Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen, Germany
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Zemann B, Le MLV, Sherlock RE, Baum D, Katija K, Stach T. Evolutionary traces of miniaturization in a giant-Comparative anatomy of brain and brain nerves in Bathochordaeus stygius (Tunicata, Appendicularia). J Morphol 2023; 284:e21598. [PMID: 37313762 DOI: 10.1002/jmor.21598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 06/15/2023]
Abstract
Appendicularia comprises 70 marine, invertebrate, chordate species. Appendicularians play important ecological and evolutionary roles, yet their morphological disparity remains understudied. Most appendicularians are small, develop rapidly, and with a stereotyped cell lineage, leading to the hypothesis that Appendicularia derived progenetically from an ascidian-like ancestor. Here, we describe the detailed anatomy of the central nervous system of Bathochordaeus stygius, a giant appendicularian from the mesopelagic. We show that the brain consists of a forebrain with on average smaller and more uniform cells and a hindbrain, in which cell shapes and sizes vary to a greater extent. Cell count for the brain was 102. We demonstrate the presence of three paired brain nerves. Brain nerve 1 traces into the epidermis of the upper lip region and consists of several fibers with some supportive bulb cells in its course. Brain nerve 2 innervates oral sensory organs and brain nerve 3 innervates the ciliary ring of the gill slits and lateral epidermis. Brain nerve 3 is asymmetric, with the right nerve consisting of two neurites originating posterior to the left one that contains three neurites. Similarities and differences to the anatomy of the brain of the model species Oikopleura dioica are discussed. We interpret the small number of cells in the brain of B. stygius as an evolutionary trace of miniaturization and conclude that giant appendicularians evolved from a small, progenetic ancestor that secondarily increased in size within Appendicularia.
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Affiliation(s)
| | - Mai-Lee Van Le
- Humboldt-Universität zu Berlin, Vergleichende Elektronenmikroskopie, Berlin, Germany
| | - Rob E Sherlock
- Monterey Bay Aquarium Research Institute, Moss Landing, California, USA
| | | | - Kakani Katija
- Monterey Bay Aquarium Research Institute, Moss Landing, California, USA
| | - Thomas Stach
- Humboldt-Universität zu Berlin, Vergleichende Elektronenmikroskopie, Berlin, Germany
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Tomholt L, Baum D, Wood RJ, Weaver JC. High-throughput segmentation, data visualization, and analysis of sea star skeletal networks. J Struct Biol 2023; 215:107955. [PMID: 36905978 DOI: 10.1016/j.jsb.2023.107955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/03/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
The remarkably complex skeletal systems of the sea stars (Echinodermata, Asteroidea), consisting of hundreds to thousands of individual elements (ossicles), have intrigued investigators for more than 150 years. While the general features and structural diversity of isolated asteroid ossicles have been well documented in the literature, the task of mapping the spatial organization of these constituent skeletal elements in a whole-animal context represents an incredibly laborious process, and as such, has remained largely unexplored. To address this unmet need, particularly in the context of understanding structure-function relationships in these complex skeletal systems, we present an integrated approach that combines micro-computed tomography, semi-automated ossicle segmentation, data visualization tools, and the production of additively manufactured tangible models to reveal biologically relevant structural data that can be rapidly analyzed in an intuitive manner. In the present study, we demonstrate this high-throughput workflow by segmenting and analyzing entire skeletal systems of the giant knobby star, Pisaster giganteus, at four different stages of growth. The in-depth analysis, presented herein, provides a fundamental understanding of the three-dimensional skeletal architecture of the sea star body wall, the process of skeletal maturation during growth, and the relationship between skeletal organization and morphological characteristics of individual ossicles. The widespread implementation of this approach for investigating other species, subspecies, and growth series has the potential to fundamentally improve our understanding of asteroid skeletal architecture and biodiversity in relation to mobility, feeding habits, and environmental specialization in this fascinating group of echinoderms.
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Affiliation(s)
- Lara Tomholt
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Harvard University Graduate School of Design, 48 Quincy St, Cambridge, MA 02138, USA
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, 14195 Berlin, Germany
| | - Robert J Wood
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - James C Weaver
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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Vohra SK, Harth P, Isoe Y, Bahl A, Fotowat H, Engert F, Hege HC, Baum D. A Visual Interface for Exploring Hypotheses about Neural Circuits. IEEE Trans Vis Comput Graph 2023; PP:1-13. [PMID: 37022819 DOI: 10.1109/tvcg.2023.3243668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa.
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Laguillo-Diego A, Kiewisz R, Martí-Gómez C, Baum D, Müller-Reichert T, Vernos I. MCRS1 modulates the heterogeneity of microtubule minus-end morphologies in mitotic spindles. Mol Biol Cell 2022; 34:ar1. [PMID: 36350698 PMCID: PMC9816640 DOI: 10.1091/mbc.e22-08-0306-t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Faithful chromosome segregation requires the assembly of a bipolar spindle, consisting of two antiparallel microtubule (MT) arrays having most of their minus ends focused at the spindle poles and their plus ends overlapping in the spindle midzone. Spindle assembly, chromosome alignment, and segregation require highly dynamic MTs. The plus ends of MTs have been extensively investigated but their minus-end structure remains poorly characterized. Here, we used large-scale electron tomography to study the morphology of the MT minus ends in three dimensionally reconstructed metaphase spindles in HeLa cells. In contrast to the homogeneous open morphology of the MT plus ends at the kinetochores, we found that MT minus ends are heterogeneous, showing either open or closed morphologies. Silencing the minus end-specific stabilizer, MCRS1 increased the proportion of open MT minus ends. Altogether, these data suggest a correlation between the morphology and the dynamic state of the MT ends. Taking this heterogeneity of the MT minus-end morphologies into account, our work indicates an unsynchronized behavior of MTs at the spindle poles, thus laying the groundwork for further studies on the complexity of MT dynamics regulation.
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Affiliation(s)
- Alejandra Laguillo-Diego
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Robert Kiewisz
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Carlos Martí-Gómez
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, 14195 Berlin, Germany
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Isabelle Vernos
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona 08003, Spain,Universitat Pompeu Fabra, Barcelona 08003, Spain,ICREA, Barcelona 08010, Spain,*Address correspondence to: Isabelle Vernos ()
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Hajarolasvadi N, Sunkara V, Khavnekar S, Beck F, Brandt R, Baum D. Volumetric macromolecule identification in cryo-electron tomograms using capsule networks. BMC Bioinformatics 2022; 23:360. [PMID: 36042418 PMCID: PMC9429335 DOI: 10.1186/s12859-022-04901-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
Background Despite recent advances in cellular cryo-electron tomography (CET), developing automated tools for macromolecule identification in submolecular resolution remains challenging due to the lack of annotated data and high structural complexities. To date, the extent of the deep learning methods constructed for this problem is limited to conventional Convolutional Neural Networks (CNNs). Identifying macromolecules of different types and sizes is a tedious and time-consuming task. In this paper, we employ a capsule-based architecture to automate the task of macromolecule identification, that we refer to as 3D-UCaps. In particular, the architecture is composed of three components: feature extractor, capsule encoder, and CNN decoder. The feature extractor converts voxel intensities of input sub-tomograms to activities of local features. The encoder is a 3D Capsule Network (CapsNet) that takes local features to generate a low-dimensional representation of the input. Then, a 3D CNN decoder reconstructs the sub-tomograms from the given representation by upsampling. Results We performed binary and multi-class localization and identification tasks on synthetic and experimental data. We observed that the 3D-UNet and the 3D-UCaps had an \documentclass[12pt]{minimal}
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\begin{document}$$F_1-$$\end{document}F1-score mostly above 60% and 70%, respectively, on the test data. In both network architectures, we observed degradation of at least 40% in the \documentclass[12pt]{minimal}
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\begin{document}$$F_1$$\end{document}F1-score when identifying very small particles (PDB entry 3GL1) compared to a large particle (PDB entry 4D8Q). In the multi-class identification task of experimental data, 3D-UCaps had an \documentclass[12pt]{minimal}
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\begin{document}$$F_1$$\end{document}F1-score of 91% on the test data in contrast to 64% of the 3D-UNet. The better \documentclass[12pt]{minimal}
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\begin{document}$$F_1$$\end{document}F1-score of 3D-UCaps compared to 3D-UNet is obtained by a higher precision score. We speculate this to be due to the capsule network employed in the encoder. To study the effect of the CapsNet-based encoder architecture further, we performed an ablation study and perceived that the \documentclass[12pt]{minimal}
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\begin{document}$$F_1$$\end{document}F1-score is boosted as network depth is increased which is in contrast to the previously reported results for the 3D-UNet. To present a reproducible work, source code, trained models, data as well as visualization results are made publicly available. Conclusion Quantitative and qualitative results show that 3D-UCaps successfully perform various downstream tasks including identification and localization of macromolecules and can at least compete with CNN architectures for this task. Given that the capsule layers extract both the existence probability and the orientation of the molecules, this architecture has the potential to lead to representations of the data that are better interpretable than those of 3D-UNet. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04901-w.
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Affiliation(s)
- Noushin Hajarolasvadi
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Takustraße 7, 14195, Berlin, Germany.
| | - Vikram Sunkara
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Takustraße 7, 14195, Berlin, Germany
| | - Sagar Khavnekar
- Department of CryoEM Technology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Florian Beck
- Department of CryoEM Technology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Robert Brandt
- Materials and Structural Analysis, Thermo Fisher Scientific, Takustraße 7, 14195, Berlin, Germany
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Takustraße 7, 14195, Berlin, Germany
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11
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Kiewisz R, Fabig G, Conway W, Baum D, Needleman DJ, Müller-Reichert T. Three-dimensional structure of kinetochore-fibers in human mitotic spindles. eLife 2022; 11:75459. [PMID: 35894209 PMCID: PMC9365394 DOI: 10.7554/elife.75459] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/24/2022] [Indexed: 11/13/2022] Open
Abstract
During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the chromosomes and the rest of the spindle. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here, we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers and their surrounding MTs in detail. We found that k-fibers exhibit remarkable variation in circumference and KMT density along their length, with the pole-proximal side showing a broadening. Extending our structural analysis then to other MTs in the spindle, we further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for KMT growth and k-fiber self-organization models as covered in a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2022). Finally, we also introduce a new visualization tool allowing an interactive display of our 3D spindle data that will serve as a resource for further structural studies on mitosis in human cells.
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Affiliation(s)
- Robert Kiewisz
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - William Conway
- Department of Physics, Harvard University, Cambridge, United States
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Daniel J Needleman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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12
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Berio F, Bayle Y, Baum D, Goudemand N, Debiais-Thibaud M. Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations. PeerJ 2022; 10:e13575. [PMID: 35811817 PMCID: PMC9261926 DOI: 10.7717/peerj.13575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/22/2022] [Indexed: 01/17/2023] Open
Abstract
Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.
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Affiliation(s)
- Fidji Berio
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS, UCBL, Lyon, France
- Institut des Sciences de l’Évolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Yann Bayle
- Université de Bordeaux, Bordeaux INP, CNRS, LaBRI, Talence, France
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Nicolas Goudemand
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS, UCBL, Lyon, France
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l’Évolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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13
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Eigen L, Baum D, Dean MN, Werner D, Wölfer J, Nyakatura JA. Ontogeny of a tessellated surface: Carapace growth of the longhorn cowfish Lactoria cornuta. J Anat 2022; 241:565-580. [PMID: 35638264 PMCID: PMC9358767 DOI: 10.1111/joa.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022] Open
Abstract
Biological armors derive their mechanical integrity in part from their geometric architectures, often involving tessellations: individual structural elements tiled together to form surface shells. The carapace of boxfish, for example, is composed of mineralized polygonal plates, called scutes, arranged in a complex geometric pattern and nearly completely encasing the body. In contrast to artificial armors, the boxfish exoskeleton grows with the fish; the relationship between the tessellation and the gross structure of the armor is therefore critical to sustained protection throughout growth. To clarify whether or how the boxfish tessellation is maintained or altered with age, we quantify architectural aspects of the tessellated carapace of the longhorn cowfish Lactoria cornuta through ontogeny (across nearly an order of magnitude in standard length) and in a high‐throughput fashion, using high‐resolution microCT data and segmentation algorithms to characterize the hundreds of scutes that cover each individual. We show that carapace growth is canalized with little variability across individuals: rather than continually adding scutes to enlarge the carapace surface, the number of scutes is surprisingly constant, with scutes increasing in volume, thickness, and especially width with age. As cowfish and their scutes grow, scutes become comparatively thinner, with the scutes at the edges (weak points in a boxy architecture) being some of the thickest and most reinforced in younger animals and thinning most slowly across ontogeny. In contrast, smaller scutes with more variable curvature were found in the limited areas of more complex topology (e.g., around fin insertions, mouth, and anus). Measurements of Gaussian and mean curvature illustrate that cowfish are essentially tessellated boxes throughout life: predominantly zero curvature surfaces comprised of mostly flat scutes, and with scutes with sharp bends used sparingly to form box edges. Since growth of a curved, tiled surface with a fixed number of tiles would require tile restructuring to accommodate the surface's changing radius of curvature, our results therefore illustrate a previously unappreciated advantage of the odd boxfish morphology: by having predominantly flat surfaces, it is the box‐like body form that in fact permits a relatively straightforward growth system of this tessellated architecture (i.e., where material is added to scute edges). Our characterization of the ontogeny and maintenance of the carapace tessellation provides insights into the potentially conflicting mechanical, geometric, and developmental constraints of this species but also perspectives into natural strategies for constructing mutable tiled architectures. The carapace of boxfish is composed of mineralized polygonal plates, called scutes, arranged in a complex geometric pattern and nearly completely encasing the body. To clarify whether or how this armor is maintained or altered with age, we quantify architectural aspects of the carapace of the longhorn cowfish Lactoria cornuta through ontogeny, using high‐resolution microCT data and segmentation algorithms to characterize the hundreds of scutes that cover each individual.![]()
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Affiliation(s)
- Lennart Eigen
- Comparative Zoology, Institute of Biology, Humboldt University of Berlin, Berlin, Germany.,Bernstein Center for Computational Neuroscience Berlin, Humboldt University of Berlin, Berlin, Germany
| | - Daniel Baum
- Visual and Data-Centric Computing Department, Zuse Institute Berlin, Berlin, Germany
| | - Mason N Dean
- Comparative Zoology, Institute of Biology, Humboldt University of Berlin, Berlin, Germany.,Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Daniel Werner
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Jan Wölfer
- Comparative Zoology, Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - John A Nyakatura
- Comparative Zoology, Institute of Biology, Humboldt University of Berlin, Berlin, Germany
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14
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Abstract
The Hemiptera, with approximately 98 000 species, is one of the largest insect orders. Most species feed by sucking sap from plant tissues and are thus often vectors for economically important phytopathogens. Well known within this group are the large cicadas (Cicadomorpha: Cicadoidea: Cicadidae) because they produce extremely loud airborne sounds. Less well known are their mostly tiny relatives, the leafhoppers, spittlebugs, treehoppers and planthoppers that communicate by silent vibrational signals. While the generation of these signals has been extensively investigated, the mechanisms of their perception are poorly understood. This study provides a complete description and three-dimensional reconstruction of a large and complex array of mechanoreceptors in the first abdominal segments of the Rhododendron leafhopper Graphocephala fennahi (Cicadomorpha: Membracoidea: Cicadellidae). Further, we identify homologous organs in the spittlebug Philaenus spumarius (Cicadomorpha: Cercopoidea: Aphrophoridae) and the planthopper Issus coleoptratus (Fulgoromorpha: Fulgoroidea: Issidae). Such large abdominal sensory arrays have not been found in any other insect orders studied so far. This indicates that these sense organs, together with the signal-producing tymbal organ, constitute a synapomorphy of the Tymbalia (Hemiptera excl. Sternorrhyncha). Our results contribute to the understanding of the evolution from substrate-borne to airborne communication in insects.
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Affiliation(s)
- Sarah Ehlers
- Centre for Integrative Biodiversity Discovery (CIBD), Museum of Natural History Berlin (MfN), Invalidenstraße 43, 10115 Berlin, Germany
| | - Daniel Baum
- Visual and Data-Centric Computing, Zuse Institute Berlin, Takustr. 7, 14195 Berlin, Germany
| | | | - Hannelore Hoch
- Centre for Integrative Biodiversity Discovery (CIBD), Museum of Natural History Berlin, Invalidenstraße 43, 10115 Berlin, Germany
| | - Peter Bräunig
- Biology Department II (Zoology), RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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15
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Lindow N, Brünig FN, Dercksen VJ, Fabig G, Kiewisz R, Redemann S, Müller-Reichert T, Prohaska S, Baum D. Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography. J Microsc 2021; 284:25-44. [PMID: 34110027 DOI: 10.1111/jmi.13039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/11/2021] [Accepted: 06/02/2021] [Indexed: 11/30/2022]
Abstract
We present a software-assisted workflow for the alignment and matching of filamentous structures across a three-dimensional (3D) stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After the computation of an initial automatic matching, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labour. The software tool was developed in an interdisciplinary collaboration between computer scientists and cell biologists to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite dealing with imperfect data related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time-consuming. Furthermore, an interactive visualisation of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialised, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. To the best of our knowledge, it is the only currently available tool which is able to process data of the type and size presented here. The key to our solution is a careful design of the visualisation and interaction tools for each processing step to guarantee real-time response, and an optimised workflow that efficiently guides the user through datasets. The final solution presented here is the result of an iterative process with tight feedback loops between the involved computer scientists and cell biologists. LAY DESCRIPTION: Electron tomography of biological samples is used for a three-dimensional (3D) reconstruction of filamentous structures, such as microtubules (MTs) in mitotic and meiotic spindles. Large-scale electron tomography can be applied to increase the reconstructed volume for the visualisation of full spindles. For this, each spindle is cut into a series of semi-thick physical sections, from which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. Previously, we presented fully automatic approaches for this 3D reconstruction pipeline. However, large volumes often suffer from imperfections (ie physical distortions) caused by the image acquisition process, making it difficult to apply fully automatic approaches for matching and stitching of numerous tomograms. Therefore, we developed an interactive, semi-automatic solution that considers all requirements for large-scale stitching of microtubules in image stacks of consecutive sections. We achieved this by combining automatic methods, visual validation and interactive error correction, thus allowing the user to continuously improve the result by interactively correcting landmarks or matches of filaments. We present large-scale reconstructions of spindles in which the automatic workflow failed and where different steps of manual corrections were needed. Our approach is also applicable to other biological samples showing 3D distributions of MTs in a number of different cellular contexts.
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Affiliation(s)
- Norbert Lindow
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Florian N Brünig
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Vincent J Dercksen
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Robert Kiewisz
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Stefanie Redemann
- School of Medicine, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia.,School of Medicine, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia.,School of Medicine, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Steffen Prohaska
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
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16
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Biron T, Baum D, Freche D, Matalon N, Ehrmann N, Weinreb E, Biron D, Moses E. Automatic detection of prosodic boundaries in spontaneous speech. PLoS One 2021; 16:e0250969. [PMID: 33939754 PMCID: PMC8092678 DOI: 10.1371/journal.pone.0250969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/16/2021] [Indexed: 11/19/2022] Open
Abstract
Automatic speech recognition (ASR) and natural language processing (NLP) are expected to benefit from an effective, simple, and reliable method to automatically parse conversational speech. The ability to parse conversational speech depends crucially on the ability to identify boundaries between prosodic phrases. This is done naturally by the human ear, yet has proved surprisingly difficult to achieve reliably and simply in an automatic manner. Efforts to date have focused on detecting phrase boundaries using a variety of linguistic and acoustic cues. We propose a method which does not require model training and utilizes two prosodic cues that are based on ASR output. Boundaries are identified using discontinuities in speech rate (pre-boundary lengthening and phrase-initial acceleration) and silent pauses. The resulting phrases preserve syntactic validity, exhibit pitch reset, and compare well with manual tagging of prosodic boundaries. Collectively, our findings support the notion of prosodic phrases that represent coherent patterns across textual and acoustic parameters.
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Affiliation(s)
- Tirza Biron
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Baum
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Dominik Freche
- Sagol Center for Brain and Mind, Interdisciplinary Center, Herzliya, Israel
| | - Nadav Matalon
- Department of Linguistics, The Hebrew University, Jerusalem, Israel
| | - Netanel Ehrmann
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal Weinreb
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - David Biron
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Elisha Moses
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
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17
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Baum D, Langanke D. Ist die brusterhaltende Therapie nach neoadjuvanter Chemotherapie sicher? Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1714516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023] Open
Affiliation(s)
- D Baum
- St. Elisabeth Krankenhaus Leipzig, Senologie
| | - D Langanke
- St. Elisabeth Krankenhaus Leipzig, Senologie
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18
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Abstract
AbstractThe images of D’Arcy Wentworth Thompson’s book “On Growth and Form” got an iconic status and became influential for biometrics and other mathematical approaches to organismic form. In particular, this is true for those of the chapter on the theory of transformation, which even has an impact on art and humanities. Based on his approach, Thompson formulated far-reaching conclusions with a partly anti-Darwinian stance. Here, we use the example of Thompson’s transformation of crab carapaces to test to what degree the transformation of grids, landmarks, and shapes result in congruent images. For comparison, we applied the same series of tests to digitized carapaces of real crabs. Both approaches show similar results. Only the simple transformations show a reasonable form of congruence. In particular, the transformations to majoid spider crabs reveal a complicated transformation of grids with partly crossing lines. By contrast, the carapace of the lithodid species is relatively easily created despite the fact that it is no brachyuran, but evolved a spider crab-like shape convergently from a hermit crab ancestor.
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19
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Schotte M, Chaumel J, Dean MN, Baum D. Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae. MethodsX 2020; 7:100905. [PMID: 32461920 PMCID: PMC7240223 DOI: 10.1016/j.mex.2020.100905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022] Open
Abstract
A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools are required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semiautomatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT.The first step of this pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required recently developed, novel tools. For error correction, we developed an interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. Finally, the tesserae and their corresponding lacunae were subdivided into structural wedges (i.e. specific anatomical regions) using a semi-manual approach.
With this processing pipeline, analysis of a variety of interconnected structural networks (e.g. vascular or lacuno-canalicular networks) can be achieved in a comparatively high-throughput fashion. In our study system, we were able to efficiently segment more than 12,000 lacunae in high-resolution scans of nine tesserae, providing a robust data set for statistical analysis.
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Affiliation(s)
- Merlind Schotte
- Visual Data Analysis Department, Zuse Institute Berlin, Takustrasse 7, 14195 Berlin, Germany
| | - Júlia Chaumel
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Mason N Dean
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Daniel Baum
- Visual Data Analysis Department, Zuse Institute Berlin, Takustrasse 7, 14195 Berlin, Germany
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20
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Chaumel J, Schotte M, Bizzarro JJ, Zaslansky P, Fratzl P, Baum D, Dean MN. Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage. Bone 2020; 134:115264. [PMID: 32058019 DOI: 10.1016/j.bone.2020.115264] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 02/06/2023]
Abstract
In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the functions of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue and that cells maintain similar volume even when they have been incorporated into tesserae. Our findings support previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes, being flatter further from and more spherical closer to the unmineralized cartilage matrix, and larger in the center of tesserae. The lacunae show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact, and that pores may contain a nutrient source. We propose that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongated series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone.
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Affiliation(s)
- Júlia Chaumel
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Merlind Schotte
- Visual Data Analysis Department, Zuse Institute Berlin, Takustrasse 7, 14195 Berlin, Germany.
| | - Joseph J Bizzarro
- Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.
| | - Paul Zaslansky
- Department for Operative and Preventive Dentistry, Universitätsmedizin Berlin, Aßmannshauser Str. 4-6 14197 Berlin, Germany.
| | - Peter Fratzl
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Daniel Baum
- Visual Data Analysis Department, Zuse Institute Berlin, Takustrasse 7, 14195 Berlin, Germany.
| | - Mason N Dean
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
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21
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Gossrau G, Baum D, Koch T, Sabatowski R, Hummel T, Haehner A. Exposure to Odors Increases Pain Threshold in Chronic Low Back Pain Patients. Pain Medicine 2020; 21:2546-2551. [DOI: 10.1093/pm/pnaa072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
Objectives
Structured exposure to odors is an acknowledged therapy in patients with smell loss but has also been shown to be effective in depression. The latter might rely on connections between olfactory and emotional structures, suggesting possible effects of a similar approach in pain patients. Based on neuroanatomy, there are several interfaces between the “pain matrix” and olfactory system, such as the limbic system, hypothalamus, and mediodorsal thalamus. We aimed to investigate whether structured exposure to odors may impact perceived pain in patients with chronic low back pain.
Design
Randomized controlled parallel-group design. Subjects were tested on two occasions, at baseline and after four weeks.
Setting
Ambulatory.
Subjects
Forty-two patients with chronic low back pain
Methods
For all patients, olfactory function (using the “Sniffin’Sticks” test kit), detection, and pain thresholds for cutaneous electrical stimuli (applied to the forearm) were tested at baseline and after four weeks. Twenty-eight patients exposed themselves to four odors (rose, vanilla, chocolate, peach) every two hours over a period of four weeks (training group). Control patients (N = 14) underwent no such “olfactory training” (nontraining group).
Results
Pain thresholds were significantly increased in patients who performed olfactory training compared with patients who did not train with odors. Detection thresholds and olfactory function remained unchanged.
Conclusions
The present results indicate that regular exposure to odors increases pain thresholds in patients with chronic back pain and could be useful for general pain control in these patients. Furthermore, olfactory training in chronic pain patients might help to reduce chronification of pain by desensitization.
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Affiliation(s)
| | - Daniel Baum
- Smell & Taste Clinic, Department of Otorhinolaryngology, TU Dresden, Dresden, Germany
| | - Thea Koch
- Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine Carl Gustav Carus, University Hospital, TU Dresden, Dresden, Germany
| | - Rainer Sabatowski
- University Pain Center, TU Dresden, Dresden, Germany
- Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine Carl Gustav Carus, University Hospital, TU Dresden, Dresden, Germany
| | - Thomas Hummel
- Smell & Taste Clinic, Department of Otorhinolaryngology, TU Dresden, Dresden, Germany
| | - Antje Haehner
- Smell & Taste Clinic, Department of Otorhinolaryngology, TU Dresden, Dresden, Germany
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22
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Baum D, Weaver JC, Zlotnikov I, Knötel D, Tomholt L, Dean MN. High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms. Integr Comp Biol 2020; 59:1700-1712. [PMID: 31282926 PMCID: PMC6907396 DOI: 10.1093/icb/icz117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e., poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e., structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, the random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies—tessellated cartilage from a stingray, the dermal endoskeleton of a starfish, and the prismatic layer of a bivalve mollusc shell—we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized, and analyzed.
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Affiliation(s)
- Daniel Baum
- Department of Visual Data Analysis, Zuse Institute Berlin, Berlin, Germany
| | - James C Weaver
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Igor Zlotnikov
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - David Knötel
- Department of Visual Data Analysis, Zuse Institute Berlin, Berlin, Germany
| | - Lara Tomholt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA.,Harvard Graduate School of Design, Harvard University, Cambridge, MA, USA
| | - Mason N Dean
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Research Campus Golm, Potsdam, Germany
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23
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Nyakatura JA, Baumgarten R, Baum D, Stark H, Youlatos D. Muscle internal structure revealed by contrast-enhanced μCT and fibre recognition: The hindlimb extensors of an arboreal and a fossorial squirrel. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Torrey H, Khodadoust M, Tran L, Baum D, Defusco A, Kim YH, Faustman DL. Targeted killing of TNFR2-expressing tumor cells and T regs by TNFR2 antagonistic antibodies in advanced Sézary syndrome. Leukemia 2018; 33:1206-1218. [PMID: 30356161 PMCID: PMC6756055 DOI: 10.1038/s41375-018-0292-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/10/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023]
Abstract
Sézary syndrome (SS) is a rare form of cutaneous T-cell lymphoma often refractory to treatment. SS is defined as adenopathy, erythroderma with high numbers of atypical T cells. This offers an opportunity for new interventions and perhaps antibody-based therapeutic by virtue of its high expression of the TNFR2 oncogene on the tumor cells and on T-regulatory cells (Tregs). Potent human-directed TNFR2 antagonistic antibodies have been created that preferentially target the TNFR2 oncogene and tumor-infiltrating TNFR2+ Tregs. Here we test the therapeutic potential of TNFR2 antagonists on freshly isolated lymphocytes from patients with Stage IVA SS and from healthy controls. SS patients were on a variety of end-stage multi-drug therapies. Baseline burden Treg/T effector (Teff) ratios and the responsiveness of tumor and infiltrating Tregs to TNFR2 antibody killing was studied. We show dose-escalating concentrations of a dominant TNFR2 antagonistic antibody killed TNFR2+ SS tumor cells and thus restored CD26- subpopulations of lymphocyte cell numbers to normal. The abundant TNFR2+ Tregs of SS subjects are also killed with TNFR2 antagonism. Beneficial and rapid expansion of Teff was observed. The combination of Treg inhibition and Teff expansion brought the high Treg/Teff ratio to normal. Our findings suggest a marked responsiveness of SS tumor cells and Tregs, to targeting with TNFR2 antagonistic antibodies. These results show TNFR2 antibodies are potent and efficacious in vitro.
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Affiliation(s)
- H Torrey
- Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street, Rm 3602, 02129, Boston, MA, USA
| | - M Khodadoust
- Stanford University School of Medicine/Cancer Institute, 94305, Palo Alto, CA, USA
| | - L Tran
- Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street, Rm 3602, 02129, Boston, MA, USA
| | - D Baum
- Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street, Rm 3602, 02129, Boston, MA, USA
| | - A Defusco
- Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street, Rm 3602, 02129, Boston, MA, USA
| | - Y H Kim
- Stanford University School of Medicine/Cancer Institute, 94305, Palo Alto, CA, USA
| | - D L Faustman
- Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street, Rm 3602, 02129, Boston, MA, USA.
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25
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Abstract
The analysis and visualization of nucleic acids (RNA and DNA) is playing an increasingly important role due to their fundamental importance for all forms of life and the growing number of known 3D structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. We present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables for the first time real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization.
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26
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Walliczek-Dworschak U, Poncelet J, Baum D, Baki R, Sinding C, Warr J, Hummel T. The Presentation of Olfactory-Trigeminal Mixed Stimuli Increases the Response to Subsequent Olfactory Stimuli. J Agric Food Chem 2018; 66:2312-2318. [PMID: 27951642 DOI: 10.1021/acs.jafc.6b04342] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The aim of this study was to evaluate the effect of (1) the addition of trigeminal stimuli to an olfactory stimulus and (2) the congruence in the odorous mixture after repeated odor presentation. Twenty-five normosmic volunteers were enrolled and presented stimulation blocks, consisting of three habituation stimuli (H) (orange odor), one dishabituation (DH) (control condition, orange odor; congruent condition, orange odor + CO2; incongruent condition, orange odor + l-isopulegol), and one dishabituated stimulus (D) (orange odor). Olfactory event-related potentials were analyzed. Response amplitudes differed significantly in the incongruent condition (N1P2 between H3 and D; peak to peak N1P2 at electrode positions Cz, Fz, and Pz; response amplitudes between H3 and DH). The addition of CO2 modified the perception of orange odor, pronouncing a fruity note, whereas the addition of l-isopulegol as a DH pronounced the l-isopulegol note. This study provides evidence that incongruent trigeminal-olfactory stimulants increase the response to subsequent olfactory stimulus.
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Affiliation(s)
- Ute Walliczek-Dworschak
- Smell & Taste Clinic, Department of Otorhinolaryngology , Technische Universität Dresden , Dresden , Germany
- Department of Otorhinolaryngology-Head and Neck Surgery , University Hospital of Marburg, University of Giessen and Marburg , Marburg , Germany
| | - Johan Poncelet
- Takasago Europe Perfumery Laboratory S.A.R.L. , Paris , France
| | - Daniel Baum
- Smell & Taste Clinic, Department of Otorhinolaryngology , Technische Universität Dresden , Dresden , Germany
| | - Ramona Baki
- Smell & Taste Clinic, Department of Otorhinolaryngology , Technische Universität Dresden , Dresden , Germany
| | - Charlotte Sinding
- Smell & Taste Clinic, Department of Otorhinolaryngology , Technische Universität Dresden , Dresden , Germany
| | - Jonathan Warr
- Takasago Europe Perfumery Laboratory S.A.R.L. , Paris , France
| | - Thomas Hummel
- Smell & Taste Clinic, Department of Otorhinolaryngology , Technische Universität Dresden , Dresden , Germany
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27
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Knötel D, Seidel R, Prohaska S, Dean MN, Baum D. Automated segmentation of complex patterns in biological tissues: Lessons from stingray tessellated cartilage. PLoS One 2017; 12:e0188018. [PMID: 29236705 PMCID: PMC5728489 DOI: 10.1371/journal.pone.0188018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 10/29/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays. Methods Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size. Results Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours.
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Affiliation(s)
- David Knötel
- Zuse Institute Berlin, Dept. of Visual Data Analysis, Berlin, Germany
- * E-mail:
| | - Ronald Seidel
- Max Planck Institute of Colloids and Interfaces, Dept. of Biomaterials, Potsdam-Golm, Germany
| | - Steffen Prohaska
- Zuse Institute Berlin, Dept. of Visual Data Analysis, Berlin, Germany
| | - Mason N. Dean
- Max Planck Institute of Colloids and Interfaces, Dept. of Biomaterials, Potsdam-Golm, Germany
| | - Daniel Baum
- Zuse Institute Berlin, Dept. of Visual Data Analysis, Berlin, Germany
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28
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Homberg U, Baum D, Prohaska S, Günster J, Krauß-Schüler S. Adapting trabecular structures for 3D printing: an image processing approach based on
μ
CT data. Biomed Phys Eng Express 2017. [DOI: 10.1088/2057-1976/aa7611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Hummel T, Fark T, Baum D, Warr J, Hummel CB, Schriever VA. The Rewarding Effect of Pictures with Positive Emotional Connotation upon Perception and Processing of Pleasant Odors-An FMRI Study. Front Neuroanat 2017; 11:19. [PMID: 28377697 PMCID: PMC5359254 DOI: 10.3389/fnana.2017.00019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/28/2017] [Indexed: 01/05/2023] Open
Abstract
This fMRI study was designed to investigate the effect of cross-modal conditioning in 28 female volunteers. Subjects underwent initial fMRI block design scanning during which three pleasant olfactory stimuli were presented and had to be rated with respect to intensity and pleasantness. This was followed by an odor identification task spread out over 3 days: the experimental group was rewarded for successful trials (correct odor identification) with emotionally salient photos, whilst the control group only received randomly displayed, emotionally neutral, pictures. In the final scanning session, the odors were again presented, and subjects rated pleasantness and intensity. Both pleasantness ratings and fMRI data showed effects of the rewarding procedure. Activation in nucleus accumbens and the orbitofrontal cortex confirmed the hypothesis that learnt association of odors with visual stimuli of emotionally positive valence not only increases pleasantness of the olfactory stimuli but is also reflected in the activation of brain structures relevant for hedonic and reward processing. To our knowledge, this is the first paper to report successful cross-modal conditioning of olfactory stimuli with visual clues.
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Affiliation(s)
- Thomas Hummel
- Smell and Taste Clinic, Department of Otorhinolaryngology, Technische Universität Dresden Dresden, Germany
| | - Therese Fark
- Smell and Taste Clinic, Department of Otorhinolaryngology, Technische Universität Dresden Dresden, Germany
| | - Daniel Baum
- Smell and Taste Clinic, Department of Otorhinolaryngology, Technische Universität Dresden Dresden, Germany
| | - Jonathan Warr
- Smell and Taste Clinic, Department of Otorhinolaryngology, Technische Universität Dresden Dresden, Germany
| | - Cornelia B Hummel
- Smell and Taste Clinic, Department of Otorhinolaryngology, Technische Universität Dresden Dresden, Germany
| | - Valentin A Schriever
- Smell and Taste Clinic, Department of Otorhinolaryngology, Technische Universität Dresden Dresden, Germany
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30
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Hug F, Goupille C, Baum D, Raiteri BJ, Hodges PW, Tucker K. Nature of the coupling between neural drive and force-generating capacity in the human quadriceps muscle. Proc Biol Sci 2016; 282:rspb.2015.1908. [PMID: 26609085 DOI: 10.1098/rspb.2015.1908] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The force produced by a muscle depends on both the neural drive it receives and several biomechanical factors. When multiple muscles act on a single joint, the nature of the relationship between the neural drive and force-generating capacity of the synergistic muscles is largely unknown. This study aimed to determine the relationship between the ratio of neural drive and the ratio of muscle force-generating capacity between two synergist muscles (vastus lateralis (VL) and vastus medialis (VM)) in humans. Twenty-one participants performed isometric knee extensions at 20 and 50% of maximal voluntary contractions (MVC). Myoelectric activity (surface electromyography (EMG)) provided an index of neural drive. Physiological cross-sectional area (PCSA) was estimated from measurements of muscle volume (magnetic resonance imaging) and muscle fascicle length (three-dimensional ultrasound imaging) to represent the muscles' force-generating capacities. Neither PCSA nor neural drive was balanced between VL and VM. There was a large (r = 0.68) and moderate (r = 0.43) correlation between the ratio of VL/VM EMG amplitude and the ratio of VL/VM PCSA at 20 and 50% of MVC, respectively. This study provides evidence that neural drive is biased by muscle force-generating capacity, the greater the force-generating capacity of VL compared with VM, the stronger bias of drive to the VL.
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Affiliation(s)
- François Hug
- School of Health and Rehabilitation Sciences, The University of Queensland, NHMRC Centre of Clinical Research Excellence in Spinal Pain, Injury and Health, Brisbane, Australia Laboratory EA 4334 'Movement, Interactions, Performance', University of Nantes, Nantes, France
| | - Clément Goupille
- Laboratory EA 4334 'Movement, Interactions, Performance', University of Nantes, Nantes, France
| | - Daniel Baum
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia, and
| | - Brent J Raiteri
- School of Human Movement and Nutrition Sciences, Centre for Sensorimotor Performance, The University of Queensland, Brisbane, Australia
| | - Paul W Hodges
- School of Health and Rehabilitation Sciences, The University of Queensland, NHMRC Centre of Clinical Research Excellence in Spinal Pain, Injury and Health, Brisbane, Australia
| | - Kylie Tucker
- School of Health and Rehabilitation Sciences, The University of Queensland, NHMRC Centre of Clinical Research Excellence in Spinal Pain, Injury and Health, Brisbane, Australia School of Biomedical Sciences, The University of Queensland, Brisbane, Australia, and
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31
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Matsuyama K, Titschack J, Baum D, Freiwald A. Two new species of erect Bryozoa (Gymnolaemata: Cheilostomata) and the application of non-destructive imaging methods for quantitative taxonomy. Zootaxa 2015; 4020:81-100. [PMID: 26624090 DOI: 10.11646/zootaxa.4020.1.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Indexed: 11/04/2022]
Abstract
Two new species of cheilostome Bryozoa are described from continental-slope habitats off Mauritania, including canyon and cold-water coral (mound) habitats. Internal structures of both species were visualised and quantified using microcomputed tomographic (micro-CT) methods. Cellaria bafouri n. sp. is characterised by the arrangement of zooids in alternating longitudinal rows, a smooth cryptocyst, and the presence of an ooecial plate with denticles. Smittina imragueni n. sp. exhibits many similarities with Smittina cervicornis (Pallas, 1766), but differs especially in the shape and orientation of the suboral avicularium. Observations on Smittina imragueni and material labelled as Smittina cervicornis suggest that the latter represents a species group, members of which have not yet been discriminated, possibly because of high intracolony variation and marked astogenetic changes in surface morphology. Both new species are known only from the habitats where they were collected, probably reflecting the paucity of bryozoan sampling from this geographic area and depth range. Both species are able to tolerate low oxygen concentration, which is assumed to be compensated by the high nutrient supply off Mauritania. The application of micro-CT for the semiautomatic quantification of zooidal skeletal characters was successfully tested. We were able to automatically distinguish individual zooidal cavities and acquire corresponding morphological datasets. Comparing the obtained results with conventional SEM measurements allowed ascertaining the reliability of this new method. The employment of micro-CT allows the observation and quantification of previously unseen characters that can be used in describing and differentiating species that were previously indistinguishable. Furthermore, this method might help elucidate processes of colony growth and the function of individual zooids during this process.
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Affiliation(s)
- Kei Matsuyama
- Senckenberg am Meer, Abteilung Meeresforschung, Südstrand 40, 26382 Wilhelmshaven, Germany.;
| | - Jürgen Titschack
- Senckenberg am Meer, Abteilung Meeresforschung, Südstrand 40, 26382 Wilhelmshaven, Germany. MARUM-Center of Marine Environmental Sciences, University of Bremen, Leobener Straße, 28359 Bremen, Germany; unknown
| | - Daniel Baum
- ZIB-Zuse Institute Berlin, Takustraße 7, 14195 Berlin-Dahlem, Germany; unknown
| | - André Freiwald
- Senckenberg am Meer, Abteilung Meeresforschung, Südstrand 40, 26382 Wilhelmshaven, Germany.; unknown
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32
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Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J Membr Biol 2015; 248:611-40. [PMID: 26063070 PMCID: PMC4515176 DOI: 10.1007/s00232-015-9802-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/26/2015] [Indexed: 01/05/2023]
Abstract
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
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Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Toby W. Allen
- School of Applied Sciences & Health Innovations Research Institute, RMIT University, GPO Box 2476, Melbourne, Vic, 3001, Australia; and Department of Chemistry, University of California, Davis. Davis, CA 95616, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Daniel Baum
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Grace Brannigan
- Center for Computational and Integrative Biology and Department of Physics, Rutgers University-Camden, Camden, NJ, USA
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Lucie Delemotte
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Coral del Val
- Department of Artificial Intelligence, University of Granada, E-18071 Granada, Spain
| | - Ran Friedman
- Linnæus University, Department of Chemistry and Biomedical Sciences & Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Paraskevi Gkeka
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Hans-Christian Hege
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, IBPC and CNRS, Paris, France
| | - Marina A. Kasimova
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Michael L. Klein
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Syma Khalid
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Norbert Lindow
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Mahua Roy
- Department of Chemistry, University of California, Irvine
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Mounir Tarek
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- CNRS, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
| | - Florentina Tofoleanu
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Sinisa Urban
- Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, 725 N. Wolfe Street, 507 Preclinical Teaching Building, Baltimore, MD 21205, USA
| | - David J. Wales
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeremy C. Smith
- Oak Ridge National Laboratory, PO BOX 2008 MS6309, Oak Ridge, TN 37831-6309, USA
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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33
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Abstract
UNLABELLED PURPOSE/AIMS OF THE STUDY: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro-computed tomography (µCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. MATERIALS AND METHODS We investigated bone during healing by means of µCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. RESULTS We present an approach for the registration of 2D data in a 3D µCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into µCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. CONCLUSIONS By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.
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Affiliation(s)
- Rebecca M Hoerth
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces , Potsdam , Germany
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Abstract
The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes - including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules.
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Weber B, Tranfield EM, Höög JL, Baum D, Antony C, Hyman T, Verbavatz JM, Prohaska S. Automated stitching of microtubule centerlines across serial electron tomograms. PLoS One 2014; 9:e113222. [PMID: 25438148 PMCID: PMC4249889 DOI: 10.1371/journal.pone.0113222] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/30/2014] [Indexed: 01/17/2023] Open
Abstract
Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts' opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.
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Affiliation(s)
- Britta Weber
- Zuse Institute Berlin, Berlin, Germany
- Max Planck Institute for Molecular Biology and Genetics, Dresden, Germany
| | | | - Johanna L. Höög
- Max Planck Institute for Molecular Biology and Genetics, Dresden, Germany
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Claude Antony
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tony Hyman
- Max Planck Institute for Molecular Biology and Genetics, Dresden, Germany
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Redemann S, Weber B, Möller M, Verbavatz JM, Hyman AA, Baum D, Prohaska S, Müller-Reichert T. The segmentation of microtubules in electron tomograms using Amira. Methods Mol Biol 2014; 1136:261-278. [PMID: 24633801 DOI: 10.1007/978-1-4939-0329-0_12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The development of automatic tools for the three-dimensional reconstruction of the microtubule cytoskeleton is crucial for large-scale analysis of mitotic spindles. Recently, we have published a method for the semiautomatic tracing of microtubules based on 3D template matching (Weber et al., J Struct Biol 178:129-138, 2012). Here, we give step-by-step instructions for the automatic tracing of microtubules emanating from centrosomes in the early mitotic Caenorhabditis elegans embryo. This approach, integrated in the visualization and data analysis software Amira, is applicable to tomographic data sets from other model systems.
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Affiliation(s)
- Stefanie Redemann
- Experimental Center, Medical Faculty Carl Gustav Carus , Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
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Homberg U, Baum D, Wiebel A, Prohaska S, Hege HC. Definition, Extraction, and Validation of Pore Structures in Porous Materials. Mathematics and Visualization 2014. [DOI: 10.1007/978-3-319-04099-8_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Abstract
Background The internal cavities of proteins are dynamic structures and their dynamics may be associated with conformational changes which are required for the functioning of the protein. In order to study the dynamics of these internal protein cavities, appropriate tools are required that allow rapid identification of the cavities as well as assessment of their time-dependent structures. Results In this paper, we present such a tool and give results that illustrate the applicability for the analysis of molecular dynamics trajectories. Our algorithm consists of a pre-processing step where the structure of the cavity is computed from the Voronoi diagram of the van der Waals spheres based on coordinate sets from the molecular dynamics trajectory. The pre-processing step is followed by an interactive stage, where the user can compute, select and visualize the dynamic cavities. Importantly, the tool we discuss here allows the user to analyze the time-dependent changes of the components of the cavity structure. An overview of the cavity dynamics is derived by rendering the dynamic cavities in a single image that gives the cavity surface colored according to its time-dependent dynamics. Conclusion The Voronoi-based approach used here enables the user to perform accurate computations of the geometry of the internal cavities in biomolecules. For the first time, it is possible to compute dynamic molecular paths that have a user-defined minimum constriction size. To illustrate the usefulness of the tool for understanding protein dynamics, we probe the dynamic structure of internal cavities in the bacteriorhodopsin proton pump.
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Kratz A, Baum D, Hotz I. Anisotropic sampling of planar and two-manifold domains for texture generation and glyph distribution. IEEE Trans Vis Comput Graph 2013; 19:1782-1794. [PMID: 24029900 DOI: 10.1109/tvcg.2013.83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We present a new method for the generation of anisotropic sample distributions on planar and two-manifold domains. Most previous work that is concerned with aperiodic point distributions is designed for isotropically shaped samples. Methods focusing on anisotropic sample distributions are rare, and either they are restricted to planar domains, are highly sensitive to the choice of parameters, or they are computationally expensive. In this paper, we present a time-efficient approach for the generation of anisotropic sample distributions that only depends on intuitive design parameters for planar and two-manifold domains. We employ an anisotropic triangulation that serves as basis for the creation of an initial sample distribution as well as for a gravitational-centered relaxation. Furthermore, we present an approach for interactive rendering of anisotropic Voronoi cells as base element for texture generation. It represents a novel and flexible visualization approach to depict metric tensor fields that can be derived from general tensor fields as well as scalar or vector fields.
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Affiliation(s)
- D Baum
- Botany Dept, University of Wisconsin, Madison, WI 53706, USA
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Weber B, Greenan G, Prohaska S, Baum D, Hege HC, Müller-Reichert T, Hyman AA, Verbavatz JM. Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos. J Struct Biol 2011; 178:129-38. [PMID: 22182731 DOI: 10.1016/j.jsb.2011.12.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 11/23/2011] [Accepted: 12/05/2011] [Indexed: 01/15/2023]
Abstract
The ability to rapidly assess microtubule number in 3D image stacks from electron tomograms is essential for collecting statistically meaningful data sets. Here we implement microtubule tracing using 3D template matching. We evaluate our results by comparing the automatically traced centerlines to manual tracings in a large number of electron tomograms of the centrosome of the early Caenorhabditis elegans embryo. Furthermore, we give a qualitative description of the tracing results for three other types of samples. For dual-axis tomograms, the automatic tracing yields 4% false negatives and 8% false positives on average. For single-axis tomograms, the accuracy of tracing is lower (16% false negatives and 14% false positives) due to the missing wedge in electron tomography. We also implemented an editor specifically designed for correcting the automatic tracing. Besides, this editor can be used for annotating microtubules. The automatic tracing together with a manual correction significantly reduces the amount of manual labor for tracing microtubule centerlines so that large-scale analysis of microtubule network properties becomes feasible.
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Affiliation(s)
- Britta Weber
- Zuse Institute Berlin, Department of Visualization and Data Analysis, Takustrasse 7, 14195 Berlin, Germany.
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Abstract
Visual analysis is widely used to study the behavior of molecules. Of particular interest are the analysis of molecular interactions and the investigation of binding sites. For large molecules, however, it is difficult to detect possible binding sites and paths leading to these sites by pure visual inspection. In this paper, we present new methods for the computation and visualization of potential molecular paths. Using a novel filtering method, we extract the significant paths from the Voronoi diagram of spheres. For the interactive visualization of molecules and their paths, we present several methods using deferred shading and other state-of-the-art techniques. To allow for a fast overview of reachable regions of the molecule, we illuminate the molecular surface using a large number of light sources placed on the extracted paths. We also provide a method to compute the extension surface of selected paths and visualize it using the skin surface. Furthermore, we use the extension surface to clip the molecule to allow easy visual tracking of even deeply buried paths. The methods are applied to several proteins to demonstrate their usefulness.
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Bakeman MS, van Tilborg J, Sokollik T, Baum D, Ybarrolaza N, Duarte R, Toth C, Leemans WP. Calibration of a microchannel plate based extreme ultraviolet grazing incident spectrometer at the Advanced Light Source. Rev Sci Instrum 2010; 81:10E313. [PMID: 21034012 DOI: 10.1063/1.3483208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present the design and calibration of a microchannel plate based extreme ultraviolet spectrometer. Calibration was performed at the Advance Light Source (ALS) at the Lawrence Berkeley National Laboratory (LBNL). This spectrometer will be used to record the single shot spectrum of radiation emitted by the tapered hybrid undulator (THUNDER) undulator installed at the LOASIS GeV-class laser-plasma-accelerator. The spectrometer uses an aberration-corrected concave grating with 1200 lines/mm covering 11-62 nm and a microchannel plate detector with a CsI coated photocathode for increased quantum efficiency in the extreme ultraviolet. A touch screen interface controls the grating angle, aperture size, and placement of the detector in vacuum, allowing for high-resolution measurements over the entire spectral range.
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Affiliation(s)
- M S Bakeman
- Department of Physics, University of Nevada Reno, Reno, Nevada 89557, USA.
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Merriman T, Twells R, Merriman M, Eaves I, Cox R, Cucca F, McKinney P, Shield J, Baum D, Bosi E, Pozzilli P, Nistico L, Buzzetti R, Joner G, Ronningen KS, Thorsby E, Undlien D, Pociot F, Nerup J, Bain S, Barnett A, Todd J. Evidence by allelic association-dependent methods for a type 1 diabetes polygene (IDDM6) on chromosome 18q21. Hum Mol Genet 2007. [DOI: 10.1093/hmg/ddm307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Baum D, Kovalenko IN. An estimate for the loss probability in a queueing system of the $MAP/G/m/0$ type in the case of light traffic. Theor Probability and Math Statist 2005. [DOI: 10.1090/s0094-9000-05-00644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Desjardins PJ, Grossman EH, Kuss ME, Talwalker S, Dhadda S, Baum D, Hubbard RC. The injectable cyclooxygenase-2-specific inhibitor parecoxib sodium has analgesic efficacy when administered preoperatively. Anesth Analg 2001; 93:721-7. [PMID: 11524347 DOI: 10.1097/00000539-200109000-00036] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Preoperative administration of analgesics may prevent or reduce hyperalgesia and inhibit inflammation and pain by reducing the synthesis of prostaglandins in response to surgical injury. We evaluated in this placebo-controlled study the analgesic efficacy and safety of single doses of parecoxib sodium (20, 40, and 80 mg IV) when administered before oral surgery. Efficacy assessments were recorded during the 24-h period after completion of surgery. All doses of parecoxib sodium were consistently and significantly superior to placebo as measured by time to rescue medication, proportion of patients requiring rescue medication, patient's global assessment, and pain intensity. There were no significant differences between the Parecoxib Sodium 40- and 80-mg groups, suggesting that the analgesic effect of preoperatively administered parecoxib sodium reaches a plateau at 40 mg in this model. Forty-eight percent of the Parecoxib Sodium 40-mg group required rescue medication in the 24-h study period, compared with 93% of patients in the Placebo group. Overall, there were fewer adverse events in parecoxib sodium-treated patients compared with placebo. These findings suggest that preoperative administration of parecoxib sodium, the injectable prodrug of the cyclooxygenase-2 specific inhibitor valdecoxib, is effective, safe, and well tolerated for treating postoperative pain.
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Kolata RJ, Ransick M, Briggs L, Baum D. Comparison of wounds created by non-bladed trocars and pyramidal tip trocars in the pig. J Laparoendosc Adv Surg Tech A 1999; 9:455-61. [PMID: 10522546 DOI: 10.1089/lap.1999.9.455] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Wounds made by the Endopath nonbladed obturator, the Step trocar, and conventional pyramidal tip trocars were compared. The endopath nonbladed obturator and the Step trocar made wounds by separating tissue fibers, whereas the pyramidal tip trocar cut tissue fibers. The wounds of the Endopath nonbladed obturator and the Step trocar were similar in length but were narrower than wounds made by the pyramidal tip trocar. Further studies are needed to determine whether the wounds made by the Endopath nonbladed obturator and the Step trocar will have fewer complications than conventional pyramidal tip trocars.
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Affiliation(s)
- R J Kolata
- Ethicon Endo-Surgery, Inc., Cincinnati, Ohio 45242, USA.
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Baum D, Yaron R, Yellin MJ. TNF-alpha, not CD154 (CD40L), plays a major role in SEB-dependent, CD4(+) T cell-induced endothelial cell activation in vitro. Cell Immunol 1998; 190:12-22. [PMID: 9826442 DOI: 10.1006/cimm.1998.1380] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
CD4(+) T cell effector molecules, in particular TNF-alpha and CD154, activate endothelial cells. However, the relative contributions of TNF-alpha and CD154 in mediating endothelial cell activation during complex Ag-driven CD4(+) T cell-endothelial cell interactions are not known. We utilized an in vitro model of CD4(+) T cell-endothelial cell interactions to characterize the contributions of TNF-alpha and CD154 in mediating upregulation of adhesion molecules CD54, CD62E, and CD106 on human umbilical vein endothelial cells (HUVEC). HUVEC were first treated with IFN-gamma to upregulate MHC Class II expression. IFN-gamma minimally effects HUVEC adhesion molecule expression but renders them capable of MHC class II restricted interactions with CD4(+) T cells. Coculturing MHC class II+ HUVEC and CD4(+) T cells with the superantigen SEB induces a rapid and marked upregulation of CD54, CD62E, and CD106 expression on HUVEC, as shown by FACS analysis. To study the effector molecules mediating SEB-driven, CD4(+) T cell-dependent endothelial cell activation, similar experiments were performed in the presence of neutralizing anti-CD154, anti-TNF-alpha, or anti-IL1 antibodies, as well as combinations of these antibodies. In contrast to the anti-CD154 or anti-IL-1 antibodies, the anti-TNF-alpha mAb markedly inhibited SEB-dependent, CD4(+) T cell-induced HUVEC activation. We conclude that TNF-alpha, not CD154, plays the major role in SEB-driven, CD4(+) T cell-induced endothelial cell activation in vitro.
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Affiliation(s)
- D Baum
- Department of Medicine, College of Physicians and Surgeons, New York, New York, 10032, USA
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Alverson W, Karol K, Baum D, Chase M, Swensen S, McCourt R, Sytsma K. Circumscription of the Malvales and relationships to other Rosidae: evidence from rbcL sequence data. Am J Bot 1998; 85:876. [PMID: 21684971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The order Malvales remains poorly circumscribed, despite its seemingly indisputable core constituents: Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae. We conducted a two-step parsimony analysis on 125 rbcL sequences to clarify the composition of Malvales, to determine the relationships of some controversial families, and to identify the placement of the Malvales within Rosidae. We sampled taxa that have been previously suggested to be within, or close to, Malvales (83 sequences), plus additional rosids (26 sequences) and nonrosid eudicots (16 sequences) to provide a broader framework for the analysis. The resulting trees strongly support the monophyly of the core malvalean families, listed above. In addition, these data serve to identify a broader group of taxa that are closely associated with the core families. This expanded malvalean clade is composed of four major subclades: (1) the core families (Bombacaceae, Malvaceae, Sterculiaceae, Tiliaceae); (2) Bixaceae, Cochlospermaceae, and Sphaerosepalaceae (Rhopalocarpaceae); (3) Thymelaeaceae sensu lato (s.l.); and (4) Cistaceae, Dipterocarpaceae s.l., Sarcolaenaceae (Chlaenaceae), and Muntingia. In addition, Neurada (Neuradaceae or Rosaceae) falls in the expanded malvalean clade but not clearly within any of the four major subclades. This expanded malvalean clade is sister to either the expanded capparalean clade of Rodman et al. or the sapindalean clade of Gadek et al. Members of Elaeocarpaceae, hypothesized by most authors as a sister group to the four core malvalean families, are shown to not fall close to these taxa. Also excluded as members of, or sister groups to, the expanded malvalean clade were the families Aextoxicaceae, Barbeyaceae, Cannabinaceae, Cecropiaceae, Dichapetalaceae, Elaeagnaceae, Euphorbiaceae s.l., Huaceae, Lecythidaceae, Moraceae s.l., Pandaceae, Plagiopteraceae, Rhamnaceae, Scytopetalaceae, Ulmaceae, and Urticaceae.
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