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Kurz A, Müller H, Kather JN, Schneider L, Bucher TC, Brinker TJ. 3-Dimensional Reconstruction From Histopathological Sections: A Systematic Review. J Transl Med 2024; 104:102049. [PMID: 38513977 DOI: 10.1016/j.labinv.2024.102049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/18/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Although pathological tissue analysis is typically performed on single 2-dimensional (2D) histologic reference slides, 3-dimensional (3D) reconstruction from a sequence of histologic sections could provide novel opportunities for spatial analysis of the extracted tissue. In this review, we analyze recent works published after 2018 and report information on the extracted tissue types, the section thickness, and the number of sections used for reconstruction. By analyzing the technological requirements for 3D reconstruction, we observe that software tools exist, both free and commercial, which include the functionality to perform 3D reconstruction from a sequence of histologic images. Through the analysis of the most recent works, we provide an overview of the workflows and tools that are currently used for 3D reconstruction from histologic sections and address points for future work, such as a missing common file format or computer-aided analysis of the reconstructed model.
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Affiliation(s)
- Alexander Kurz
- Digital Biomarkers for Oncology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heimo Müller
- Diagnostics and Research Institute for Pathology, Medical University of Graz, Graz, Austria
| | - Jakob N Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Lucas Schneider
- Digital Biomarkers for Oncology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tabea C Bucher
- Digital Biomarkers for Oncology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Titus J Brinker
- Digital Biomarkers for Oncology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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2
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Mendoza JCE, Chan KO, Lai JCY, Thoma BP, Clark PF, Guinot D, Felder DL, Ng PKL. A comprehensive molecular phylogeny of the brachyuran crab superfamily Xanthoidea provides novel insights into its systematics and evolutionary history. Mol Phylogenet Evol 2022; 177:107627. [PMID: 36096461 DOI: 10.1016/j.ympev.2022.107627] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
Maximum likelihood and Bayesian phylogenies for the brachyuran crab superfamily Xanthoidea were estimated based on three mitochondrial and four nuclear genes to infer phylogenetic relationships and inform taxonomy. Habitat data was then used in conjunction with several diversification rates analyses (BAMM, BiSSE, HiSSE, and FiSSE) to test evolutionary hypotheses regarding the diversification of xanthoid crabs. The phylogenies presented are the most comprehensive to date in terms of global diversity as they include all four constituent families (Xanthidae, Panopeidae, Pseudorhombilidae, and Linnaeoxanthidae) spanning all oceans in which xanthoid crabs occur. Six Xanthoidea families are recognised. Panopeidae and Xanthidae sensu stricto are the two largest family-level clades, which are reciprocally monophyletic. Pseudorhombilidae is nested within and is here treated as a subfamily of Panopeidae. Former subfamilies or tribes of Xanthidae sensu lato are basally positioned clades in Xanthoidea and are here assigned family-level ranks: Garthiellidae, Linnaeoxanthidae, Antrocarcinidae, and Nanocassiopidae. The genera Linnaeoxantho and Melybia were recovered in separate clades with Linnaeoxantho being sister to the family Antrocarcinidae, while Melybia was recovered within the family Panopeidae. The existing subfamily classification of Xanthidae and Panopeidae is drastically restructured with 20 xanthid and four panopeid subfamilies provisionally recognised. Diversification-time analyses inferred the origin of Xanthoidea and Garthiellidae in the Eocene, while the other families originated during the Oligocene. The majority of genus- and species-level diversification took place during the Miocene. Ancestral state reconstruction based on depth of occurrence (shallow vs. deep water) shows some ambiguity for the most recent common ancestor of Xanthoidea and Nanocassiopidae. The most recent common ancestors of Antrocarcinidae and Panopeidae were likely deep-water species, while those of Garthiellidae and Xanthidae were probably shallow-water species. Several shifts in net diversification rates were detected but they were not associated with depth-related habitat transitions.
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Affiliation(s)
- Jose C E Mendoza
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore, Singapore.
| | - Kin Onn Chan
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore, Singapore.
| | - Joelle C Y Lai
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore, Singapore
| | - Brent P Thoma
- Department of Biology, Jackson State University, P.O. Box 18540, Jackson, MS 39217, USA
| | - Paul F Clark
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Danièle Guinot
- Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Institut de Systématique, Évolution, Biodiversité (ISYEB), Case Postale 53, 57 rue Cuvier, F-75231 Paris cedex 05, France
| | - Darryl L Felder
- Department of Biology and Laboratory for Crustacean Research, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Peter K L Ng
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore, Singapore
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Luque J, Feldmann RM, Vernygora O, Schweitzer CE, Cameron CB, Kerr KA, Vega FJ, Duque A, Strange M, Palmer AR, Jaramillo C. Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony. SCIENCE ADVANCES 2019; 5:eaav3875. [PMID: 31032408 PMCID: PMC6482010 DOI: 10.1126/sciadv.aav3875] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
Evolutionary origins of novel forms are often obscure because early and transitional fossils tend to be rare, poorly preserved, or lack proper phylogenetic contexts. We describe a new, exceptionally preserved enigmatic crab from the mid-Cretaceous of Colombia and the United States, whose completeness illuminates the early disparity of the group and the origins of novel forms. Its large and unprotected compound eyes, small fusiform body, and leg-like mouthparts suggest larval trait retention into adulthood via heterochronic development (pedomorphosis), while its large oar-like legs represent the earliest known adaptations in crabs for active swimming. Our phylogenetic analyses, including representatives of all major lineages of fossil and extant crabs, challenge conventional views of their evolution by revealing multiple convergent losses of a typical "crab-like" body plan since the Early Cretaceous. These parallel morphological transformations may be associated with repeated invasions of novel environments, including the pelagic/necto-benthic zone in this pedomorphic chimera crab.
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Affiliation(s)
- J. Luque
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Smithsonian Tropical Research Institute, Balboa-Ancón 0843-03092, Panamá, Panamá
- Department of Geology and Geophysics, Yale University, New Haven, CT 06520-8109, USA
| | - R. M. Feldmann
- Department of Geology, Kent State University, Kent, OH 44242, USA
| | - O. Vernygora
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - C. E. Schweitzer
- Department of Geology, Kent State University at Stark, 6000 Frank Ave. NW, North Canton, OH 44720, USA
| | - C. B. Cameron
- Département de Sciences Biologiques Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - K. A. Kerr
- Smithsonian Tropical Research Institute, Balboa-Ancón 0843-03092, Panamá, Panamá
- Canadian Parks and Wilderness Society (CPAWS) Northern Alberta, P.O. Box 52031, Edmonton, AB T6G 2T5, Canada
| | - F. J. Vega
- Instituto de Geología, Universidad Autónoma de México, Ciudad Universitaria, México, CDMX 04510, México
| | - A. Duque
- Computer Animation and Visual Effects, College of Communication and Design, Lynn University, 2601 North Military Trail, Boca Raton, FL 33431, USA
| | - M. Strange
- Department of Geoscience, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4010, USA
| | - A. R. Palmer
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - C. Jaramillo
- Smithsonian Tropical Research Institute, Balboa-Ancón 0843-03092, Panamá, Panamá
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Garcia Bento MA, López Greco LS, Zara FJ. Seminal fluid production and sperm packaging in dromiid crabs (Brachyura, Podotremata). ZOOLOGY 2018; 132:17-30. [PMID: 30736926 DOI: 10.1016/j.zool.2018.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 11/24/2022]
Abstract
Reproductive anatomy, including sperm storage structures and sperm transfer, is an important feature used to analyze phylogenetic relationships among taxa. We describe the male reproductive anatomy, seminal fluid production and packaging of spermatozoa in the vas deferens of primitive crabs. In all species of Dromiidae, the testes were tubular type and the vas deferens is a tube with a simple epithelium. The spermatozoa are in a central mass immersed in type I secretion, forming a large spermatic cord. In Moreiradromia antillensis and Dromia erythropus the spermatic cord is surrounded by a more complex secretion layer composed by protein granules and polysaccharides that seem to be responsible to form the sperm plaque which was absent in Hypoconcha. The sperm plaque was found in all Dromiinae species, which may result from the mating and probably act as a barrier to subsequent copulations. These patterns of elongated coenospermic spermatophore found here are unique and different from the spermatophores of all true crabs and may be considered a plesiomorphic state to spermatophoric structure in Brachyura. Our results show a novel type of spermatozoa packaging and new insights into how sperm might be transferred in Podotremata.
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Affiliation(s)
- Maria Alice Garcia Bento
- Universidade Estadual Paulista (UNESP), FCAV, Laboratório de Morfologia de Invertebrados (IML), Departamento de Biologia Aplicada à Agropecuária e Centro de Aquicultura da Unesp (CAUNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, 14884-900, São Paulo, Brasil.
| | - Laura S López Greco
- Universidad de Buenos Aires, CONICET, Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Laboratorio de Biología de la Reproducción y el Crecimiento de Crustáceos Decápodos, C1428EGA, Buenos Aires, Argentina.
| | - Fernando José Zara
- Universidade Estadual Paulista (UNESP), FCAV, Laboratório de Morfologia de Invertebrados (IML), Departamento de Biologia Aplicada à Agropecuária e Centro de Aquicultura da Unesp (CAUNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, 14884-900, São Paulo, Brasil; Universidade Estadual Paulista (UNESP), IB, Avenida 24 A, 1515, Rio Claro, 13506-900, São Paulo, Brasil.
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Kienbaum K, Vehof J, Becker C, Scholtz G. The reproductive system of Limnopilos naiyanetri indicates a thoracotreme affiliation of Hymenosomatidae (Decapoda, Eubrachyura). ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:513-520. [PMID: 29966700 DOI: 10.1016/j.asd.2018.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
The eubrachyuran Hymenosomatoidea is widely distributed in tropical and subtropical regions ranging from marine to freshwater habitats. Even though the biology of this taxon has been studied to some extent, its phylogenetic relationships are not resolved. Based on different morphological characters, some authors suggested a close affinity of hymenosomatid crabs to heterotremes. However, many of these characters are ambiguous, and the few molecular studies did not provide convincing solutions either. To address this issue, we studied the reproductive system of the hymenosomatid freshwater species Limnopilos naiyanetri Chuang and Ng, 1991 using histology and scanning electron microscopy. The females show the characteristic organization of the paired eubrachyuran reproductive system. Additionally, a bursa (an accessory sperm storing cuticle cavity) is present. The male copulatory system is characterized by paired long first and short second gonopods, and a pair of sternal gonopores equipped with a penis. Both, the female and male reproductive organs reveal a number of similarities to thoracotreme crabs. The seminal receptacle is lined by a very thin cuticle and by a mono-layered glandular epithelium. The male gonopods and the sternal genital opening also resemble the thoracotreme condition. Thus, our results indicate that Hymenosomatidae are most likely part of the Thoracotremata.
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Affiliation(s)
- Katja Kienbaum
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany.
| | - Juliane Vehof
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany.
| | - Carola Becker
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany.
| | - Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany; Cluster of Excellence, "Image Knowledge Gestaltung", Humboldt-Universität zu Berlin, Sophienstr. 22a, 10178 Berlin, Germany.
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6
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Kienbaum K, Scholtz G, Becker C. The morphology of the reproductive system in the crab Percnon gibbesi
(Decapoda: Brachyura: Grapsoidea) reveals a new combination of characters in Thoracotremata. J Morphol 2018; 279:883-894. [DOI: 10.1002/jmor.20818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/17/2018] [Accepted: 03/02/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Katja Kienbaum
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie; Berlin 10115 Germany
| | - Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie; Berlin 10115 Germany
- Cluster of Excellence “Image Knowledge Gestaltung”, Humboldt-Universität zu Berlin; Berlin 10178 Germany
| | - Carola Becker
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie; Berlin 10115 Germany
- Cluster of Excellence “Image Knowledge Gestaltung”, Humboldt-Universität zu Berlin; Berlin 10178 Germany
- Queen's University Marine Laboratory; Portaferry Northern Ireland BT22 1PF UK
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