1
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Eyal Z, Deis R, Varsano N, Dezorella N, Rechav K, Houben L, Gur D. Plate-like Guanine Biocrystals Form via Templated Nucleation of Crystal Leaflets on Preassembled Scaffolds. J Am Chem Soc 2022; 144:22440-22445. [PMID: 36469805 DOI: 10.1021/jacs.2c11136] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Controlling the morphology of crystalline materials is challenging, as crystals have a strong tendency toward thermodynamically stable structures. Yet, organisms form crystals with distinct morphologies, such as the plate-like guanine crystals produced by many terrestrial and aquatic species for light manipulation. Regulation of crystal morphogenesis was hypothesized to entail physical growth restriction by the surrounding membrane, combined with fine-tuned interactions between organic molecules and the growing crystal. Using cryo-electron tomography of developing zebrafish larvae, we found that guanine crystals form via templated nucleation of thin leaflets on preassembled scaffolds made of 20-nm-thick amyloid fibers. These leaflets then merge and coalesce into a single plate-like crystal. Our findings shed light on the biological regulation of crystal morphogenesis, which determines their optical properties.
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Affiliation(s)
- Zohar Eyal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rachael Deis
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Neta Varsano
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nili Dezorella
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lothar Houben
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dvir Gur
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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2
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Gur D, Bain EJ, Johnson KR, Aman AJ, Pasolli HA, Flynn JD, Allen MC, Deheyn DD, Lee JC, Lippincott-Schwartz J, Parichy DM. Author Correction: In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning. Nat Commun 2022; 13:4330. [PMID: 35882864 PMCID: PMC9325738 DOI: 10.1038/s41467-022-32152-z] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Dvir Gur
- HHMI Janelia Research Campus, Ashburn, VA, USA.,National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Emily J Bain
- Department of Biology, University of Virginia, Charlottesville, VA, USA.,Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | - Kory R Johnson
- Bioinformatics Section, National Institute of Neurological Disorder and Stroke, NIH, Bethesda, MD, USA
| | - Andy J Aman
- Department of Biology, University of Virginia, Charlottesville, VA, USA.,Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Jessica D Flynn
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Michael C Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Dimitri D Deheyn
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer C Lee
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | | | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, VA, USA.
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3
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Gur D, Bain EJ, Johnson KR, Aman AJ, Pasoili HA, Flynn JD, Allen MC, Deheyn DD, Lee JC, Lippincott-Schwartz J, Parichy DM. In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning. Nat Commun 2020; 11:6391. [PMID: 33319779 PMCID: PMC7738553 DOI: 10.1038/s41467-020-20088-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 05/12/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Skin color patterns are ubiquitous in nature, impact social behavior, predator avoidance, and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on light-reflecting cells called iridophores. It was suggested that the zebrafish’s color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. However, here we find that iridophores do not migrate between stripes and interstripes but instead differentiate and proliferate in-place, based on their micro-environment. RNA-sequencing analysis further reveals that stripe and interstripe iridophores have different transcriptomic states, while cryogenic-scanning-electron-microscopy and micro-X-ray diffraction identify different crystal-arrays architectures, indicating that stripe and interstripe iridophores are different cell types. Based on these results, we present an alternative model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized, physiologically responsive, organelles arise in stripe and interstripe by in-situ differentiation. The skin of zebrafish is patterned by alternating blue stripes and yellow interstripes which arises from guanine crystal-containing cells called iridophores that reflect light. Here the authors track iridophores and see that they do not migrate between stripes and interstripes, but instead differentiate and proliferate in place based on their micro-environment.
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Affiliation(s)
- Dvir Gur
- HHMI Janelia Research Campus, Ashburn, VA, USA.,National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Emily J Bain
- Department of Biology, University of Virginia, Charlottesville, VA, USA.,Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | - Kory R Johnson
- Bioinformatics Section, National Institute of Neurological Disorder and Stroke, NIH, Bethesda, MD, USA
| | - Andy J Aman
- Department of Biology, University of Virginia, Charlottesville, VA, USA.,Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Jessica D Flynn
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Michael C Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Dimitri D Deheyn
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer C Lee
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | | | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, VA, USA.
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4
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Gordon L, Blechman J, Shimoni E, Gur D, Anand-Apte B, Levkowitz G. The fenestrae-associated protein Plvap regulates the rate of blood-borne protein passage into the hypophysis. Development 2019; 146:dev.177790. [PMID: 31740533 DOI: 10.1242/dev.177790] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/08/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022]
Abstract
To maintain body homeostasis, endocrine systems must detect and integrate blood-borne peripheral signals. This is mediated by fenestrae, specialized permeable pores in the endothelial membrane. Plasmalemma vesicle-associated protein (Plvap) is located in the fenestral diaphragm and is thought to play a role in the passage of proteins through the fenestrae. However, this suggested function has yet to be demonstrated directly. We studied the development of fenestrated capillaries in the hypophysis, a major neuroendocrine interface between the blood and brain. Using a transgenic biosensor to visualize the vascular excretion of the genetically tagged plasma protein DBP-EGFP, we show that the developmental acquisition of vascular permeability coincides with differential expression of zebrafish plvap orthologs in the hypophysis versus brain. Ultrastructural analysis revealed that plvapb mutants display deficiencies in fenestral diaphragms and increased density of hypophyseal fenestrae. Measurements of DBP-EGFP extravasation in plvapb mutants provided direct proof that Plvap limits the rate of blood-borne protein passage through fenestrated endothelia. We present the regulatory role of Plvap in the development of blood-borne protein detection machinery at a neuroendocrine interface through which hormones are released to the general circulation.
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Affiliation(s)
- Ludmila Gordon
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Janna Blechman
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Eyal Shimoni
- Chemical Research Support, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Dvir Gur
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Bela Anand-Apte
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic Foundation, Cleveland OH 444195, USA
| | - Gil Levkowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
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5
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Kariko S, Timonen JVI, Weaver JC, Gur D, Marks C, Leiserowitz L, Kolle M, Li L. Structural origins of coloration in the spider Phoroncidia rubroargentea Berland, 1913 (Araneae: Theridiidae) from Madagascar. J R Soc Interface 2019; 15:rsif.2017.0930. [PMID: 29467259 DOI: 10.1098/rsif.2017.0930] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 12/11/2017] [Accepted: 01/30/2018] [Indexed: 11/12/2022] Open
Abstract
This study investigates the structural basis for the red, silver and black coloration of the theridiid spider, Phoroncidia rubroargentea (Berland, 1913) from Madagascar. Specimens of this species can retain their colour after storage in ethanol for decades, whereas most other brightly pigmented spider specimens fade under identical preservation conditions. Using correlative optical, structural and chemical analysis, we identify the colour-generating structural elements and characterize their optical properties. The prominent silvery appearance of the spider's abdomen results from regularly arranged guanine microplatelets, similar to those found in other spiders and fish. The microplatelets are composed of a doublet structure twinned about the [[Formula: see text]] axis, as suggested by electron diffraction. The red coloration originates from chambered microspheres (approx. 1 µm in diameter), which contain structured fluorescent material. Co-localization of the red microparticles on top of the reflective guanine microplatelets appears to enhance the red coloration. The spider's thick cuticular layer, which encases its abdomen, varies in its optical properties, being transparent in regions where only guanine reflectors are present, and tanned, exhibiting light absorption where the red microspheres are found. Moreover, colour degradation in some preserved spider specimens that had suffered damage to the cuticular layer suggests that this region of the exoskeleton may play an important role in the stabilization of the red coloration.
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Affiliation(s)
- Sarah Kariko
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Jaakko V I Timonen
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.,Department of Applied Physics, Aalto University School of Science, Espoo 02150, Finland
| | - James C Weaver
- Wyss Institute for Biologically Inspired Technology, Harvard University, Cambridge, MA 02138, USA
| | - Dvir Gur
- Department of Physics of Complex Systems and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Carolyn Marks
- Center for Nano Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Leslie Leiserowitz
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mathias Kolle
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ling Li
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA 24060, USA
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6
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Lewis VM, Saunders LM, Larson TA, Bain EJ, Sturiale SL, Gur D, Chowdhury S, Flynn JD, Allen MC, Deheyn DD, Lee JC, Simon JA, Lippincott-Schwartz J, Raible DW, Parichy DM. Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores. Proc Natl Acad Sci U S A 2019; 116:11806-11811. [PMID: 31138706 PMCID: PMC6575160 DOI: 10.1073/pnas.1901021116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates, derived from embryonic neural crest, are a useful system for elucidating mechanisms of fate specification, pattern formation, and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes, including the zebrafish Danio rerio, we identified two populations of white pigment cells-leucophores-one of which arises by transdifferentiation of adult melanophores and another of which develops from a yellow-orange xanthophore or xanthophore-like progenitor. Single-cell transcriptomic, mutational, chemical, and ultrastructural analyses of zebrafish leucophores revealed cell-type-specific chemical compositions, organelle configurations, and genetic requirements. At the organismal level, we identified distinct physiological responses of leucophores during environmental background matching, and we showed that leucophore complement influences behavior. Together, our studies reveal independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution.
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Affiliation(s)
- Victor M Lewis
- Department of Biology, University of Virginia, Charlottesville, VA 22903
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Lauren M Saunders
- Department of Biology, University of Virginia, Charlottesville, VA 22903
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195
| | - Tracy A Larson
- Department of Biology, University of Virginia, Charlottesville, VA 22903
| | - Emily J Bain
- Department of Biology, University of Virginia, Charlottesville, VA 22903
| | | | - Dvir Gur
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
- Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Sarwat Chowdhury
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Jessica D Flynn
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Michael C Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Dimitri D Deheyn
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jennifer C Lee
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Julian A Simon
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | | | - David W Raible
- Department of Biology, University of Washington, Seattle, WA 98195
- Department of Biological Structure, University of Washington, Seattle, WA 98195
| | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, VA 22903;
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22903
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7
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Palmer BA, Gur D, Weiner S, Addadi L, Oron D. The Organic Crystalline Materials of Vision: Structure-Function Considerations from the Nanometer to the Millimeter Scale. Adv Mater 2018; 30:e1800006. [PMID: 29888511 DOI: 10.1002/adma.201800006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/07/2018] [Indexed: 06/08/2023]
Abstract
Vision mechanisms in animals, especially those living in water, are diverse. Many eyes have reflective elements that consist of multilayers of nanometer-sized crystalline plates, composed of organic molecules. The crystal multilayer assemblies owe their enhanced reflectivity to the high refractive indices of the crystals in preferred crystallographic directions. The high refractive indices are due to the molecular arrangements in their crystal structures. Herein, data regarding these difficult-to-characterize crystals are reviewed. This is followed by a discussion on the function of these crystalline assemblies, especially in visual systems whose anatomy has been well characterized under close to in vivo conditions. Three test cases are presented, and then the relations between the reflecting crystalline components and their functions, including the relations between molecular structure, crystal structure, and reflecting properties are discussed. Some of the underlying mechanisms are also discussed, and finally open questions in the field are identified.
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Affiliation(s)
- Benjamin A Palmer
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dvir Gur
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Steve Weiner
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Lia Addadi
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dan Oron
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 7610001, Israel
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8
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Tsarfati Y, Rosenne S, Weissman H, Shimon LJW, Gur D, Palmer BA, Rybtchinski B. Crystallization of Organic Molecules: Nonclassical Mechanism Revealed by Direct Imaging. ACS Cent Sci 2018; 4:1031-1036. [PMID: 30159400 PMCID: PMC6107864 DOI: 10.1021/acscentsci.8b00289] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Indexed: 05/04/2023]
Abstract
Organic crystals are of primary importance in pharmaceuticals, functional materials, and biological systems; however, organic crystallization mechanisms are not well-understood. It has been recognized that "nonclassical" organic crystallization from solution involving transient amorphous precursors is ubiquitous. Understanding how these precursors evolve into crystals is a key challenge. Here, we uncover the crystallization mechanisms of two simple aromatic compounds (perylene diimides), employing direct structural imaging by cryogenic electron microscopy. We reveal the continuous evolution of density, morphology, and order during the crystallization of very different amorphous precursors (well-defined aggregates and diffuse dense liquid phase). Crystallization starts from initial densification of the precursors. Subsequent evolution of crystalline order is gradual, involving further densification concurrent with optimization of molecular ordering and morphology. These findings may have implications for the rational design of organic crystals.
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Affiliation(s)
- Yael Tsarfati
- Department
of Organic Chemistry, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Shaked Rosenne
- Department
of Organic Chemistry, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Haim Weissman
- Department
of Organic Chemistry, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Linda J. W. Shimon
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Dvir Gur
- Departments
of Physics of Complex Systems and Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Benjamin A. Palmer
- Department
of Structural Biology, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Boris Rybtchinski
- Department
of Organic Chemistry, Weizmann Institute
of Science, Rehovot 76100, Israel
- E-mail:
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9
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Gur D, Nicolas J, Brumfeld V, Bar‐Elli O, Oron D, Levkowitz G. The Dual Functional Reflecting Iris of the Zebrafish. Adv Sci (Weinh) 2018; 5:1800338. [PMID: 30128243 PMCID: PMC6097150 DOI: 10.1002/advs.201800338] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/12/2018] [Indexed: 05/28/2023]
Abstract
Many marine organisms have evolved a reflective iris to prevent unfocused light from reaching the retina. The fish iris has a dual function, both to camouflage the eye and serving as a light barrier. Yet, the physical mechanism that enables this dual functionality and the benefits of using a reflective iris have remained unclear. Using synchrotron microfocused diffraction, cryo-scanning electron microscopy imaging, and optical analyses on zebrafish at different stages of development, it is shown that the complex optical response of the iris is facilitated by the development of high-order organization of multilayered guanine-based crystal reflectors and pigments. It is further demonstrated how the efficient light reflector is established during development to allow the optical functionality of the eye, already at early developmental stages.
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Affiliation(s)
- Dvir Gur
- Department of Physics of Complex SystemsWeizmann Institute of ScienceRehovot7610001Israel
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Jan‐David Nicolas
- Institute for X‐Ray PhysicsUniversity of GöttingenGöttingen37077Germany
| | - Vlad Brumfeld
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovot7610001Israel
| | - Omri Bar‐Elli
- Department of Physics of Complex SystemsWeizmann Institute of ScienceRehovot7610001Israel
| | - Dan Oron
- Department of Physics of Complex SystemsWeizmann Institute of ScienceRehovot7610001Israel
| | - Gil Levkowitz
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovot7610001Israel
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10
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Palmer BA, Taylor GJ, Brumfeld V, Gur D, Shemesh M, Elad N, Osherov A, Oron D, Weiner S, Addadi L. The image-forming mirror in the eye of the scallop. Science 2017; 358:1172-1175. [DOI: 10.1126/science.aam9506] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/25/2017] [Accepted: 10/23/2017] [Indexed: 11/02/2022]
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11
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Hirsch A, Palmer BA, Elad N, Gur D, Weiner S, Addadi L, Kronik L, Leiserowitz L. Biologically Controlled Morphology and Twinning in Guanine Crystals. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201704801] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Anna Hirsch
- Department of Materials and Interfaces; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Benjamin A. Palmer
- Department of Structural Biology; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Nadav Elad
- Department of Chemical Research Support; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Dvir Gur
- Departments of Molecular Cell Biology and of Physics of Complex Systems; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Steve Weiner
- Department of Structural Biology; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Lia Addadi
- Department of Structural Biology; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Leeor Kronik
- Department of Materials and Interfaces; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Leslie Leiserowitz
- Department of Materials and Interfaces; Weizmann Institute of Science; Rehovoth 76100 Israel
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12
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Hirsch A, Palmer BA, Elad N, Gur D, Weiner S, Addadi L, Kronik L, Leiserowitz L. Biologically Controlled Morphology and Twinning in Guanine Crystals. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Hirsch
- Department of Materials and Interfaces; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Benjamin A. Palmer
- Department of Structural Biology; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Nadav Elad
- Department of Chemical Research Support; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Dvir Gur
- Departments of Molecular Cell Biology and of Physics of Complex Systems; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Steve Weiner
- Department of Structural Biology; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Lia Addadi
- Department of Structural Biology; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Leeor Kronik
- Department of Materials and Interfaces; Weizmann Institute of Science; Rehovoth 76100 Israel
| | - Leslie Leiserowitz
- Department of Materials and Interfaces; Weizmann Institute of Science; Rehovoth 76100 Israel
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13
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Palmer BA, Taylor GJ, Brumeld V, Gur D, Shemesh M, Elad N, Osherov A, Oron D, Weiner S, Addadi L. Biologically controlled crystal growth: the image-forming mirror in the eye of the scallop. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317097045] [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: 11/10/2022] Open
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14
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Torumkuney D, Gur D, Soyletir G, Gurler N, Aktas Z, Sener B, Tunger A, Bayramoglu G, Koksal I, Yalcin AN, Tanriver Y, Morrissey I, Barker K. Results from the Survey of Antibiotic Resistance (SOAR) 2002-09 in Turkey. J Antimicrob Chemother 2016; 71 Suppl 1:i85-91. [PMID: 27048585 DOI: 10.1093/jac/dkw067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To investigate changes in antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae from the Survey of Antibiotic Resistance (SOAR) in community-acquired respiratory tract infections (CA-RTIs) between 2002 and 2009 in Turkey. METHODS Previously published SOAR data were used for this analysis. MICs were determined using Etest(®) gradient strips or disc diffusion. Susceptibility against a range of antimicrobial agents was assessed using CLSI breakpoints. RESULTS A total of 900 S. pneumoniae isolates were analysed: 2002-03 (n = 75), 2004-05 (n = 301) and 2007-09 (n = 524). Four antibiotics were tested consistently throughout and three showed a statistically significant decrease in susceptibility (P < 0.0001): penicillin (74.7% susceptible in 2002-03; 67.8% in 2004-05; and 47.2% in 2007-09); cefaclor (85.3% in 2002-03; 78.7% in 2004-05; and 53.5% in 2007-09) and clarithromycin (85.3% in 2002-03; 82.7% in 2004-05; and 61.9% in 2007-09). Susceptibility to amoxicillin/clavulanic acid did not significantly change (100% in 2002-03; 98.7% in 2004-05; and 97.7% in 2007-09). A total of 930 H. influenzae isolates were analysed: 2002-03 (n = 133), 2004-05 (n = 379) and 2007-09 (n = 418). Four antibiotics were also consistently tested: ampicillin, amoxicillin/clavulanic acid, clarithromycin and cefaclor. All showed >90% susceptibility, but only cefaclor susceptibility significantly reduced (P < 0.0001) over time (99.2% in 2002-03; 96.3% in 2004-05; and 90.4% in 2007-09). CONCLUSIONS In S. pneumoniae from Turkey, there has been a clear statistically significant reduction in susceptibility to key antibiotics since 2002, but not to amoxicillin/clavulanic acid (or amoxicillin). However, susceptibility in H. influenzae remained stable. Continued surveillance is required to monitor future changes in antibiotic susceptibility for CA-RTI bacteria.
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Affiliation(s)
- D Torumkuney
- GlaxoSmithKline, 980 Great West Road, Brentford, Middlesex TW8 9GS, UK
| | - D Gur
- Hacettepe University Medical Faculty, Department of Medical Microbiology, Ankara, Turkey
| | - G Soyletir
- Marmara University Medical Faculty, Department of Medical Microbiology, Istanbul, Turkey
| | - N Gurler
- Istanbul University, Istanbul Medical Faculty, Department of Medical Microbiology, Istanbul, Turkey
| | - Z Aktas
- Istanbul University, Istanbul Medical Faculty, Department of Medical Microbiology, Istanbul, Turkey
| | - B Sener
- Hacettepe University Medical Faculty, Department of Medical Microbiology, Ankara, Turkey
| | - A Tunger
- Ege University Medical Faculty, Department of Medical Microbiology, Izmir, Turkey
| | - G Bayramoglu
- Karadeniz Technical University Faculty of Medicine, Department of Infectious Diseases and Clinical Microbiology, Trabzon, Turkey
| | - I Koksal
- Karadeniz Technical University Faculty of Medicine, Department of Infectious Diseases and Clinical Microbiology, Trabzon, Turkey
| | - A N Yalcin
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Y Tanriver
- GlaxoSmithKline Turkey, Buyukdere Cad. 1. Levent Plaza, No. 173, B Blok, 34394 Istanbul, Turkey
| | - I Morrissey
- IHMA Europe Sàrl, 9A route de la Corniche, Epalinges 1066, Switzerland
| | - K Barker
- GlaxoSmithKline, 980 Great West Road, Brentford, Middlesex TW8 9GS, UK
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Soyletir G, Altinkanat G, Gur D, Altun B, Tunger A, Aydemir S, Kayacan C, Aktas Z, Gunaydin M, Karadag A, Gorur H, Morrissey I, Torumkuney D. Results from the Survey of Antibiotic Resistance (SOAR) 2011-13 in Turkey. J Antimicrob Chemother 2016; 71 Suppl 1:i71-83. [PMID: 27048584 DOI: 10.1093/jac/dkw075] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Data are presented from the Survey of Antibiotic Resistance (SOAR) for respiratory tract infection pathogens collected in 2011-13 from Turkey. METHODS MICs were determined using Etest(®). Susceptibility was assessed using CLSI, EUCAST and pharmacokinetic/pharmacodynamic (PK/PD) interpretive criteria. RESULTS Rates of antibiotic susceptibility were very low among 333 isolates of Streptococcus pneumoniae tested: penicillin 38% using CLSI (oral) and EUCAST breakpoints; erythromycin 51% using CLSI and EUCAST criteria; and cefuroxime 64.6% using CLSI and PK/PD and 46.9% using EUCAST. Of the isolates, >90% were susceptible to amoxicillin/clavulanic acid, ceftriaxone (except using EUCAST criteria: 76%), levofloxacin and high-dose intravenous penicillin. Among 339 Haemophilus influenzae isolates, 6.8% were β-lactamase positive while 9.1% were β-lactamase negative but ampicillin resistant (BLNAR) by CLSI (14.7% by EUCAST) criteria. Amoxicillin/clavulanic acid susceptibility was ∼90% by CLSI (with or without BLNAR adjustment, EUCAST and high-dose PK/PD) but lower, at 82.9%, by EUCAST with BLNAR adjustment. Levofloxacin susceptibility was 96% using all three breakpoints. Dramatic differences in rates of susceptibility, depending on the breakpoints used, were seen for cefaclor [94% by CLSI (86.4% BLNAR adjusted), 23% by PK/PD] and cefuroxime [97% by CLSI (89.1% BLNAR adjusted), 85% by PK/PD, 15% by EUCAST (13.0% BLNAR adjusted)]. Streptococcus pyogenes (n = 222) and Moraxella catarrhalis (n = 40) isolates remained highly susceptible to amoxicillin/clavulanic acid, cephalosporins and levofloxacin, with only erythromycin susceptibility dropping below 95% for S. pyogenes. CONCLUSIONS Overall, amoxicillin/clavulanic acid and levofloxacin were the most active antibiotics based on all three breakpoints against these pathogens. Although susceptibility was not universally low in Turkey, high resistance rates were found in S. pneumoniae and, when using PK/PD and EUCAST breakpoints, in other respiratory pathogens.
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Affiliation(s)
- G Soyletir
- Marmara University Medical Faculty, Department of Medical Microbiology, Istanbul, Turkey
| | - G Altinkanat
- Marmara University Medical Faculty, Department of Medical Microbiology, Istanbul, Turkey
| | - D Gur
- Hacettepe University Medical Faculty, Department of Medical Microbiology, Ankara, Turkey
| | - B Altun
- Hacettepe University Medical Faculty, Department of Medical Microbiology, Ankara, Turkey
| | - A Tunger
- Ege University Medical Faculty, Department of Medical Microbiology, Izmir, Turkey
| | - S Aydemir
- Ege University Medical Faculty, Department of Medical Microbiology, Izmir, Turkey
| | - C Kayacan
- Istanbul University, Istanbul Medical Faculty, Department of Medical Microbiology, Istanbul, Turkey
| | - Z Aktas
- Istanbul University, Istanbul Medical Faculty, Department of Medical Microbiology, Istanbul, Turkey
| | - M Gunaydin
- Ondokuz Mayıs University Medical Faculty, Department of Medical Microbiology, Samsun, Turkey
| | - A Karadag
- Ondokuz Mayıs University Medical Faculty, Department of Medical Microbiology, Samsun, Turkey
| | - H Gorur
- GlaxoSmithKline Turkey, Buyukdere Cad. 1. Levent Plaza, No. 173, B Blok, 34394, Istanbul, Turkey
| | - I Morrissey
- IHMA Europe Sàrl, 9A route de la Corniche, Epalinges 1066, Switzerland
| | - D Torumkuney
- GlaxoSmithKline, 980 Great West Road, Brentford, Middlesex TW8 9GS, UK
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Rez P, Aoki T, March K, Gur D, Krivanek OL, Dellby N, Lovejoy TC, Wolf SG, Cohen H. Erratum: Damage-free vibrational spectroscopy of biological materials in the electron microscope. Nat Commun 2016; 7:11592. [PMID: 27143477 PMCID: PMC4857455 DOI: 10.1038/ncomms11592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Rez P, Aoki T, March K, Gur D, Krivanek OL, Dellby N, Lovejoy TC, Wolf SG, Cohen H. Damage-free vibrational spectroscopy of biological materials in the electron microscope. Nat Commun 2016; 7:10945. [PMID: 26961578 PMCID: PMC4792949 DOI: 10.1038/ncomms10945] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [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: 09/17/2015] [Accepted: 02/04/2016] [Indexed: 12/11/2022] Open
Abstract
Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be ‘safely' investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope. Use of electron microscopy to determine morphology, or find where functionally significant biomolecules are located with high spatial resolution is of great interest. Here, Rez, Cohen et al. use aloof electron beam vibrational spectroscopy to probe different bonds in biological samples with no significant radiation damage.
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Affiliation(s)
- Peter Rez
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Toshihiro Aoki
- LeRoy Eyring Center for Solid State Science, Arizona State University, Tempe, Arizona 85287, USA
| | - Katia March
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, UMR8502, Orsay 91405, France
| | - Dvir Gur
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ondrej L Krivanek
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.,Nion Co., 11511 NE 118th St., Kirkland, Washington 98034, USA
| | - Niklas Dellby
- Nion Co., 11511 NE 118th St., Kirkland, Washington 98034, USA
| | - Tracy C Lovejoy
- Nion Co., 11511 NE 118th St., Kirkland, Washington 98034, USA
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hagai Cohen
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
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Gur D, Leshem B, Pierantoni M, Farstey V, Oron D, Weiner S, Addadi L. Structural Basis for the Brilliant Colors of the Sapphirinid Copepods. J Am Chem Soc 2015; 137:8408-11. [DOI: 10.1021/jacs.5b05289] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Viviana Farstey
- The Interuniversity Institute for Marine Sciences, Eilat 88103, Israel
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Gur D, Palmer BA, Leshem B, Oron D, Fratzl P, Weiner S, Addadi L. The Mechanism of Color Change in the Neon Tetra Fish: a Light-Induced Tunable Photonic Crystal Array. Angew Chem Int Ed Engl 2015; 54:12426-30. [DOI: 10.1002/anie.201502268] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/13/2015] [Indexed: 11/11/2022]
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Gur D, Palmer BA, Leshem B, Oron D, Fratzl P, Weiner S, Addadi L. The Mechanism of Color Change in the Neon Tetra Fish: a Light-Induced Tunable Photonic Crystal Array. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502268] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Gur D, Shimon LJW. Crystal structure of disodium 2-amino-6-oxo-6,7-di-hydro-1H-purine-1,7-diide hepta-hydrate. Acta Crystallogr E Crystallogr Commun 2015; 71:281-3. [PMID: 25844188 PMCID: PMC4350748 DOI: 10.1107/s2056989015003163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/13/2015] [Indexed: 11/28/2022]
Abstract
In the title compound, the deprotonated guanine molecules are arranged in centrosymmetric pairs, and form hydrogen bonds with the neighboring water molecules. In the title compound, disodium 2-amino-6-oxo-6,7-dihydro-1H-purine-1,7-diide heptahydrate, 2Na+·C5H3N5O2−·7H2O, the structure is composed of alternating (100) layers of guanine molecules and hydrated Na+ ions. Within the guanine layer, the molecules are arranged in centrosymmetric pairs, with a partial overlap between the guanine rings. In this compound, guanine exists as the amino–keto tautomer from which deprotonation from N1 and N7 has occurred (purine numbering). There are no direct interactions between the Na+ cations and the guanine anions. Guanine molecules are linked to neighboring water molecules by O—H⋯N and O—H⋯O hydrogen bonds into a network structure.
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Affiliation(s)
- Dvir Gur
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Linda J W Shimon
- Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
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Gur D, Leshem B, Oron D, Weiner S, Addadi L. The Structural Basis for Enhanced Silver Reflectance in Koi Fish Scale and Skin. J Am Chem Soc 2014; 136:17236-42. [DOI: 10.1021/ja509340c] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dvir Gur
- Departments of † Structural Biology and ‡Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ben Leshem
- Departments of † Structural Biology and ‡Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dan Oron
- Departments of † Structural Biology and ‡Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Steve Weiner
- Departments of † Structural Biology and ‡Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lia Addadi
- Departments of † Structural Biology and ‡Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
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Gur D, Hascelik G, Aydin N, Telli M, Gültekin M, Ögünç D, Arikan O, Uysal S, Yaman A, Kibar F, Gülay Z, Sumerkan B, Esel D, Kayacan C, Aktas Z, Soyletir G, Altinkanat G, Durupinar B, Darka O, Akgün Y, Yayla B, Gedikoglu S, Sinirtas M, Berktas M, Yaman G. Antimicrobial Resistance in Gram-Negative Hospital Isolates: Results of the Turkish HITIT-2 Surveillance Study of 2007. J Chemother 2013; 21:383-9. [DOI: 10.1179/joc.2009.21.4.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Gal A, Habraken W, Gur D, Fratzl P, Weiner S, Addadi L. Calcite Crystal Growth by a Solid-State Transformation of Stabilized Amorphous Calcium Carbonate Nanospheres in a Hydrogel. Angew Chem Int Ed Engl 2013; 52:4867-70. [DOI: 10.1002/anie.201210329] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/07/2013] [Indexed: 12/28/2022]
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Gal A, Habraken W, Gur D, Fratzl P, Weiner S, Addadi L. Calcite Crystal Growth by a Solid-State Transformation of Stabilized Amorphous Calcium Carbonate Nanospheres in a Hydrogel. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210329] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Gur D, Politi Y, Sivan B, Fratzl P, Weiner S, Addadi L. Guanine-Based Photonic Crystals in Fish Scales Form from an Amorphous Precursor. Angew Chem Int Ed Engl 2012; 52:388-91. [DOI: 10.1002/anie.201205336] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Indexed: 11/11/2022]
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Gur D, Politi Y, Sivan B, Fratzl P, Weiner S, Addadi L. Guanine-Based Photonic Crystals in Fish Scales Form from an Amorphous Precursor. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205336] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [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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Mahamid J, Sharir A, Gur D, Zelzer E, Addadi L, Weiner S. Bone mineralization proceeds through intracellular calcium phosphate loaded vesicles: a cryo-electron microscopy study. J Struct Biol 2011; 174:527-35. [PMID: 21440636 DOI: 10.1016/j.jsb.2011.03.014] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 03/18/2011] [Accepted: 03/18/2011] [Indexed: 11/16/2022]
Abstract
Bone is the most widespread mineralized tissue in vertebrates and its formation is orchestrated by specialized cells - the osteoblasts. Crystalline carbonated hydroxyapatite, an inorganic calcium phosphate mineral, constitutes a substantial fraction of mature bone tissue. Yet key aspects of the mineral formation mechanism, transport pathways and deposition in the extracellular matrix remain unidentified. Using cryo-electron microscopy on native frozen-hydrated tissues we show that during mineralization of developing mouse calvaria and long bones, bone-lining cells concentrate membrane-bound mineral granules within intracellular vesicles. Elemental analysis and electron diffraction show that the intracellular mineral granules consist of disordered calcium phosphate, a highly metastable phase and a potential precursor of carbonated hydroxyapatite. The intracellular mineral contains considerably less calcium than expected for synthetic amorphous calcium phosphate, suggesting the presence of a cellular mechanism by which phosphate entities are first formed and thereafter gradually sequester calcium within the vesicles. We thus demonstrate that in vivo osteoblasts actively produce disordered mineral packets within intracellular vesicles for mineralization of the extracellular developing bone tissue. The use of a highly disordered precursor mineral phase that later crystallizes within an extracellular matrix is a strategy employed in the formation of fish fin bones and by various invertebrate phyla. This therefore appears to be a widespread strategy used by many animal phyla, including vertebrates.
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Affiliation(s)
- Julia Mahamid
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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Zheng B, Sumkin JH, Zuley ML, Lederman D, Wang X, Gur D. Computer-aided detection of breast masses depicted on full-field digital mammograms: a performance assessment. Br J Radiol 2011; 85:e153-61. [PMID: 21343322 DOI: 10.1259/bjr/51461617] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVES To investigate the feasibility of converting a computer-aided detection (CAD) scheme for digitised screen-film mammograms to full-field digital mammograms (FFDMs) and assessing CAD performance on a large database. METHODS The database included 6478 FFDM images acquired on 1120 females, with 525 cancer cases and 595 negative cases. The database was divided into five case groups: (1) cancer detected during screening, (2) interval cancers, (3) "high-risk" recommended for surgical excision, (4) recalled but negative and (5) negative (not recalled). A previously developed CAD scheme for masses depicted on digitised images was converted and re-optimised for FFDM images while keeping the same image-processing structure. CAD performance was analysed on the entire database. RESULTS The case-based sensitivity was 75.6% (397/525) for the current mammograms and 40.8% (42/103) for the prior mammograms deemed negative during clinical interpretation but "visible" during retrospective review. The region-based sensitivity was 58.1% (618/1064) for the current mammograms and 28.4% (57/201) for the prior mammograms. The CAD scheme marked 55.7% (221/397) and 35.7% (15/42) of the masses on both views of the current and the prior examinations, respectively. The overall CAD-cued false-positive rate was 0.32 per image, ranging from 0.29 to 0.51 for the five case groups. CONCLUSION This study indicated that (1) digitised image-based CAD can be converted for FFDMs while performing at a comparable, or better, level; (2) CAD detects a substantial fraction of cancers depicted on prior examinations, albeit most having been marked only on one view; and (3) CAD tends to mark more false-positive results on "difficult" negative cases that are more visually difficult for radiologists to interpret.
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Affiliation(s)
- B Zheng
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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Kovo M, Weissman A, Gur D, Levran D, Rotmensch S, Glezerman M. Neonatal outcome in polycystic ovarian syndrome patients treated with metformin during pregnancy. J Matern Fetal Neonatal Med 2009; 19:415-9. [PMID: 16923696 DOI: 10.1080/14767050600682370] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [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: 10/24/2022]
Abstract
OBJECTIVE The present study aimed to evaluate the effect of metformin exposure during pregnancy on neonates of polycystic ovarian syndrome (PCOS) patients. METHOD Neonatal outcomes of 33 women with PCOS treated with metformin during pregnancy were compared to neonatal outcomes of 66 normal healthy women in a retrospective case-control study. RESULTS The mean birth weight percentile of neonates exposed to metformin in utero during the first trimester was significantly lower than that of neonates delivered to normal healthy matched controls. After controlling for pregnancy complications, this observation became only marginally statistically significant. CONCLUSION Although metformin is an attractive option for induction of ovulation in PCOS patients, there is a need for more evidence related to its safety during pregnancy.
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Affiliation(s)
- Michal Kovo
- Department of Obstetrics and Gynecology, The Edith Wolfson Medical Center, Holon, Israel.
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Lurie S, Gur D, Sadan O, Glezerman M. Relationship between uterine contractions and serum magnesium levels in patients treated for threatened preterm labour with intravenous magnesium sulphate. J OBSTET GYNAECOL 2009; 24:247-8. [PMID: 15203617 DOI: 10.1080/01443610410001660715] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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: 10/26/2022]
Abstract
We aimed to correlate the assessment of preterm uterine activity with serum magnesium levels in women with threatened preterm labour. The observational study involved twelve women receiving intravenous magnesium sulphate for threatened preterm labour. Mean gestational age at initiation of therapy was 26.9+/-2.9 weeks. Mean cervical dilatation at initiation of therapy was 1.5 cm. Serum magnesium levels and evaluation of uterine contractions by external tocograph were assessed twice daily. Presence or absence of contractions was analysed for correlation with plasma magnesium levels. Eighty-eight measurements were analysed. The mean serum magnesium levels were 1.9+/-0.5 mmol/l and 1.9+/-0.3 mmol/l in the presence (n=22) or absence (n=66) of contractions, respectively. The difference did not reach statistical significance. No correlation was found between serum magnesium levels and presence of contractions (P=0.3, logistic regression odds ratio 1.1, 95% confidence interval of 0.6-2.0). The abolition of premature uterine contractions during intravenous magnesium sulphate therapy does not correlate with serum magnesium levels.
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Affiliation(s)
- S Lurie
- Department of Obstetrics and Gynaecology, Edith Wolson Medical Center, Holon, Israel.
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Yildirim I, Ceyhan M, Gur D, Mugnaioli C, Rossolini GM. First detection of VIM-1 type metallo-beta-lactamase in a multidrug-resistant Klebsiella pneumoniae clinical isolate from Turkey also producing the CTX-M-15 extended-spectrum beta-lactamase. J Chemother 2007; 19:467-8. [PMID: 17855196 DOI: 10.1179/joc.2007.19.4.467] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Yildirim I, Ceyhan M, Gur D, Mugnaioli C, Rossolini G. R2147 First detection of VIM-1 type metallo-β-lactamase in a multidrug-resistant Klebsiella pneumoniae clinical isolate from Turkey also producing the CTX-M-15 extended-spectrum β-lactamase. Int J Antimicrob Agents 2007. [DOI: 10.1016/s0924-8579(07)71986-6] [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: 10/23/2022]
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Biedenbach D, Gur D, Korten V, Soyletir G, Jones R. P759 High-level multidrug-resistance among viridians group streptococci isolated from Turkey: report from the SENTRY Antimicrobial Surveillance Program. Int J Antimicrob Agents 2007. [DOI: 10.1016/s0924-8579(07)70600-3] [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: 11/25/2022]
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Erdem B, Ercis S, Hascelik G, Gur D, Aysev AD. Antimicrobial resistance of Salmonella enterica group C strains isolated from humans in Turkey, 2000–2002. Int J Antimicrob Agents 2005; 26:33-7. [PMID: 15953709 DOI: 10.1016/j.ijantimicag.2005.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Accepted: 03/10/2005] [Indexed: 11/20/2022]
Abstract
Fifty-three Salmonella enterica group C isolates obtained from various human samples (47 stool, 4 blood and 2 urine) in ten provinces of Turkey between 1 July 2000 and 30 June 2002 were serotyped and resistance to antimicrobials was investigated by agar dilution tests. The isolates were identified as S. Choleraesuis (11), S. Hadar (7), S. Irumu (4), S. Virchow (3), S. Tallahassee (3), S. Paratyphi C (2), S. Braenderup (2), S. Othmarschen (2), S. Menston (2), S. Concord (2), S. Infantis (2), S. Kottbus (2), S. Edinburg (1), S. Oranienburg (1), S. Muenchen (1) and S. Malmoe (1). Antimicrobial resistance rates of S. enterica groups C1 and C2 were high for ampicillin (26% and 60%, respectively), amoxicillin/clavulanic acid (11% and 40%), chloramphenicol (16% and 27%) and tetracycline (3% and 40%). The percentages of strains sensitive to all antimicrobials were 58% and 33%, respectively. Multiresistance was not observed in group C1 isolates, but the rate of multiresistant isolates was 13% in group C2. The rate of decreased ciprofloxacin susceptibility (CipL) was 61% in serogroup C1 and 20% in serogroup C2. These results indicated that S. enterica group C infections in humans were not infrequent in Turkey and that multiple antimicrobial resistance was common within these strains.
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Affiliation(s)
- B Erdem
- Department of Microbiology and Clinical Microbiology, Ankara University School of Medicine, Bilkent 3 Konutlari, F3 Blok, No. 42, Bilkent, 06800 Ankara, Turkey.
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Gur D. TU-D-I-609-03: Computer-Aided Detection (CAD) in the Laboratory and the Clinical Environment. Med Phys 2005. [DOI: 10.1118/1.1999709] [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: 11/07/2022] Open
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Erdem B, Ercis S, Hascelik G, Gur D, Gedikoglu S, Aysev AD, Sumerkan B, Tatman-Otkun M, Tuncer I. Antimicrobial resistance patterns and serotype distribution among Salmonella enterica strains in Turkey, 2000?2002. Eur J Clin Microbiol Infect Dis 2005; 24:220-5. [PMID: 15772822 DOI: 10.1007/s10096-005-1293-y] [Citation(s) in RCA: 14] [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: 10/25/2022]
Abstract
Since Turkey currently lacks a national reference center for Salmonella infections, the present study was conducted to document the distribution of serotypes and antimicrobial resistance patterns among Salmonella enterica isolates recovered from clinical samples in ten Turkish provinces over a 2-year period. Among the 620 Salmonella enterica isolates recovered between 1 July 2000 and 30 June 2002, strains belonging to the serotypes Enteritidis (47.7%), Typhimurium (34.7%), Paratyphi B (6.0%), Typhi (2.9%), Paratyphi A (0.2%) and serogroup C (8.5%) were found. Resistance to multiple antimicrobial agents was particularly high among Salmonella Typhimurium isolates (76.7%), and resistance or decreased susceptibility to ciprofloxacin (MIC> or =0.125 mg/l) was demonstrated in Salmonella Paratyphi B, Salmonella Typhimurium and Salmonella Enteritidis strains. All of the Salmonella Typhi isolates were susceptible to ciprofloxacin. The results indicate that decreased susceptibility to ciprofloxacin is an emerging problem in Salmonella enterica in Turkey, particularly in multiresistant strains.
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Affiliation(s)
- B Erdem
- Department of Microbiology and Clinical Microbiology, Ankara University School of Medicine, Ankara, Turkey.
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Gur D, Sumkin JH, Rockette HE. RESPONSE: Re: Changes in Breast Cancer Detection and Mammography Recall Rates After the Introduction of a Computer-Aided Detection System. J Natl Cancer Inst 2004. [DOI: 10.1093/jnci/djh258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Affiliation(s)
- Samuel Lurie
- Department of Obstetrics and Gynecology, Edith Wolfson Medical Center, Holon, Israel
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Rosin D, Bank I, Gayer G, Rimon U, Gur D, Kuriansky Y, Morag B, Pras M, Ayalon A. Laparoscopic splenectomy for torsion of wandering spleen associated with celiac axis occlusion. Surg Endosc 2002; 16:1110. [PMID: 12165835 DOI: 10.1007/s00464-001-0078-3] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/1999] [Accepted: 12/16/1999] [Indexed: 10/27/2022]
Abstract
BACKGROUND Wandering spleen is a spleen lacking its normal ligamentous attachments, and thus subjected to free movement in the abdominal cavity, and even torsion around its pedicle. Surgical treatment includes either fixation (splenopexy) or resection (splenectomy). Both procedures can now be accomplished using the laparoscopic approach. METHODS AND RESULTS We describe a case of a torsion of a wandering spleen, leading to recurrent episodes of abdominal pain, and eventually to splenic ischemia, necessitating splenectomy. The diagnosis was complicated by associated angiographic findings of celiac axis occlusion, possibly by median arcuate ligament compression. Laparoscopic splenectomy was successful, and led to complete resolution of symptoms. CONCLUSIONS Although a rare condition, wandering spleen can be diagnosed accurately by imaging studies, mainly CT scan and angiography. Nowadays, the laparoscopic approach is preferred and enables the surgeon to perform either splenopexy or splenectomy, depending on the vascular status of the spleen.
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Affiliation(s)
- D Rosin
- Department of General Surgery and Transplantation, Sheba Medical Center, Tel Hashomer, Israel.
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Zheng B, Ganott MA, Britton CA, Hakim CM, Hardesty LA, Chang TS, Rockette HE, Gur D. Soft-copy mammographic readings with different computer-assisted detection cuing environments: preliminary findings. Radiology 2001; 221:633-40. [PMID: 11719657 DOI: 10.1148/radiol.2213010308] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [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] [Indexed: 11/11/2022]
Abstract
PURPOSE To assess the performance of radiologists in the detection of masses and microcalcification clusters on digitized mammograms by using different computer-assisted detection (CAD) cuing environments. MATERIALS AND METHODS Two hundred nine digitized mammograms depicting 57 verified masses and 38 microcalcification clusters in 85 positive and 35 negative cases were interpreted independently by seven radiologists using five display modes. Except for the first mode, for which no CAD results were provided, suspicious regions identified with a CAD scheme were cued in all the other modes by using a combination of two cuing sensitivities (90% and 50%) and two false-positive rates (0.5 and 2.0 per image). A receiver operating characteristic study was performed by using soft-copy images. RESULTS CAD cuing at 90% sensitivity and a rate of 0.5 false-positive region per image improved observer performance levels significantly (P < .01). As accuracy of CAD cuing decreased so did observer performances (P < .01). Cuing specificity affected mass detection more significantly, while cuing sensitivity affected detection of microcalcification clusters more significantly (P < .01). Reduction of cuing sensitivity and specificity significantly increased false-negative rates in noncued areas (P < .05). Trends were consistent for all observers. CONCLUSION CAD systems have the potential to significantly improve diagnostic performance in mammography. However, poorly performing schemes could adversely affect observer performance in both cued and noncued areas.
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Affiliation(s)
- B Zheng
- Division of Imaging Research, Department of Radiology, University of Pittsburgh, 300 Halket St, Suite 4200, Pittsburgh, PA 15213, USA.
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Zheng B, Chang YH, Good WF, Gur D. Performance gain in computer-assisted detection schemes by averaging scores generated from artificial neural networks with adaptive filtering. Med Phys 2001; 28:2302-8. [PMID: 11764037 DOI: 10.1118/1.1412240] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [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: 11/07/2022] Open
Abstract
The authors investigated a new method to optimize artificial neural networks (ANNs) with adaptive filtering used in computer-assisted detection schemes in digitized mammograms and to assess performance changes when averaging classification scores from three sets of optimized schemes. Two independent training and testing image databases involving 978 and 830 digitized mammograms, respectively, were used in this study. In the training data set, initial filtering and subtraction resulted in the identification of 592 mass regions and 3790 suspicious, but actually negative regions. These regions (including both true-positive and negative regions) were segmented into three subsets three times based on the calculation of the values of three features as segmentation indices. The indices were "mass" size multiplied by their digital value contrast, conspicuity, and circularity. Nine ANN-based classifiers were separately optimized using a genetic algorithm for each subset of regions. Each region was assigned three classification scores after applying the three adaptive ANNs. The performance gain of the CAD scheme after averaging the three scores for each suspicious region was tested using an independent data set and a ROC methodology. The experimental results showed that the areas under ROC curves (Az) for the testing database using three sets of optimized ANNs individually were 0.84+/-0.01, 0.83+/-0.01, and 0.84+/-0.01, respectively. The between-index correlations of three A values were 0.013, -0.007, and 0.086. Similar to averaging diagnostic ratings from independent observers, by averaging three ANN-generated scores for each testing region, the performance of the CAD scheme was significantly improved (p<0.001) with Az value of 0.95+/-0.01.
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Affiliation(s)
- B Zheng
- Department of Radiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
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Abstract
We propose a principled formulation of the ROC curve that is constrained in a realistic way by the mechanism of probability summation. The constrained and conventional ROC formulations were fitted to 150 separate sets of rating data taken from previous observer studies of 250 or 529 chest radiographs. A total of 20 different readers had used either discrete or continuous rating scales to evaluate those chest cases for likelihood of separate specified abnormalities: interstitial disease, pulmonary nodule, pneumothorax, alveolar infiltrate, or rib fracture. Both ROC formulations were fitted separately to every set of rating data using maximum-likelihood statistical procedures that specified each ROC curve by normally distributed latent variables with two scaling parameters, and estimated the area below the ROC curve (Az) with its standard error. The conventional and constrained binormal formulations usually fitted ROC curves that were nearly indistinguishable in form and in Az. But when fitted to asymmetric rating data that contained few false-positive cases, the conventional ROC curves often rose steeply, then flattened and extrapolated into an unrealistic upward "hook" at the higher false-positive rates. For those sets of rating data, the constrained ROC curves (without hooks) estimated larger values for Az with smaller standard errors. The constrained ROC formulation describes observers' ratings of cases at least as well as the conventional ROC, and always guarantees a realistic fitted curve for observer performance. Its estimated parameters are easy to interpret, and may also be used to predict observer accuracy in localizing the image abnormalities.
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Affiliation(s)
- R G Swensson
- Department of Radiology, University of Pittsburgh, Pennsylvania 15261, USA
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Chang YH, Hardesty LA, Hakim CM, Chang TS, Zheng B, Good WF, Gur D. Knowledge-based computer-aided detection of masses on digitized mammograms: a preliminary assessment. Med Phys 2001; 28:455-61. [PMID: 11339741 DOI: 10.1118/1.1359250] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [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] [Indexed: 11/07/2022] Open
Abstract
The purpose of this work was to develop and evaluate a computer-aided detection (CAD) scheme for the improvement of mass identification on digitized mammograms using a knowledge-based approach. Three hundred pathologically verified masses and 300 negative, but suspicious, regions, as initially identified by a rule-based CAD scheme, were randomly selected from a large clinical database for development purposes. In addition, 500 different positive and 500 negative regions were used to test the scheme. This suspicious region pruning scheme includes a learning process to establish a knowledge base that is then used to determine whether a previously identified suspicious region is likely to depict a true mass. This is accomplished by quantitatively characterizing the set of known masses, measuring "similarity" between a suspicious region and a "known" mass, then deriving a composite "likelihood" measure based on all "known" masses to determine the state of the suspicious region. To assess the performance of this method, receiver-operating characteristic (ROC) analyses were employed. Using a leave-one-out validation method with the development set of 600 regions, the knowledge-based CAD scheme achieved an area under the ROC curve of 0.83. Fifty-one percent of the previously identified false-positive regions were eliminated, while maintaining 90% sensitivity. During testing of the 1,000 independent regions, an area under the ROC curve as high as 0.80 was achieved. Knowledge-based approaches can yield a significant reduction in false-positive detections while maintaining reasonable sensitivity. This approach has the potential of improving the performance of other rule-based CAD schemes.
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Affiliation(s)
- Y H Chang
- Department of Radiology, University of Pittsburgh, Pennsylvania 15261-0001, USA
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Abstract
RATIONALE AND OBJECTIVES Rank-order experiments often provide a reasonable method of determining whether a large-scale receiver operating characteristic study can be justified. The authors' purpose was to formalize a proposed method for analyzing rank-order imaging experiments and provide methods that can be used in determining sample sizes for both cases and raters. MATERIALS AND METHODS Simulations were conducted to determine the adequacy of the normal approximation of a statistic used to test the null hypothesis of random ordering. For a multireader experiment, formulas are presented and guidelines are provided to enable investigators to determine the number of required readers (raters) and cases for a specific study. RESULTS When there are at least five ordered images per case, 10 cases are sufficient to test a random rank order. When there are only three or four images for a case, 20 cases are required. The authors constructed tables of statistical power for selected numbers of ordered images, numbers of cases, and degrees of trend, and they also provide an approximation for use in situations that are not tabled. CONCLUSION The statistical methods for analyzing rank-order experiments and estimating sample sizes for study planning are relatively simple to implement. The derived formulas for sample size estimation, when applied to typical imaging experiments, indicate that modest numbers of cases and readers are required for rank-order studies.
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Affiliation(s)
- H E Rockette
- Department of Biostatistics, University of Pittsburgh, PA 15213, USA
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Zheng B, Sumkin JH, Good WF, Maitz GS, Chang YH, Gur D. Applying computer-assisted detection schemes to digitized mammograms after JPEG data compression: an assessment. Acad Radiol 2000; 7:595-602. [PMID: 10952109 DOI: 10.1016/s1076-6332(00)80574-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [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: 11/15/2022]
Abstract
RATIONALE AND OBJECTIVES The authors' purpose was to assess the effects of Joint Photographic Experts Group (JPEG) image data compression on the performance of computer-assisted detection (CAD) schemes for the detection of masses and microcalcification clusters on digitized mammograms. MATERIALS AND METHODS This study included 952 mammograms that were digitized and compressed with a JPEG-compatible image-compression scheme. A CAD scheme, previously developed in the authors' laboratory and optimized for noncompressed images, was applied to reconstructed images after compression at five levels. The performance was compared with that obtained with the original noncompressed digitized images. RESULTS For mass detection, there were no significant differences in performance between noncompressed and compressed images for true-positive regions (P = .25) or false-positive regions (P = .40). In all six modes the scheme identified 80% of masses with less than one false-positive region per image. For the detection of microcalcification clusters, there was significant performance degradation (P < .001) at all compression levels. Detection sensitivity was reduced by 4%-10% as compression ratios increased from 17:1 to 62:1. At the same time, the false-positive detection rate was increased by 91%-140%. CONCLUSION The JPEG algorithm did not adversely affect the performance of the CAD scheme for detecting masses, but it did significantly affect the detection of microcalcification clusters.
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Affiliation(s)
- B Zheng
- Department of Radiology, University of Pittsburgh, PA 15261-0001, USA
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Abstract
Six radiologists used continuous scales to rate 529 chest-film cases for likelihood of five different types of abnormalities (interstitial disease, nodule, pneumothorax, alveolar infiltrate, and rib fracture) in each of six replicated readings, yielding 36 separate ratings of each case for the five abnormalities. Separate data analyses of all cases and subsets of the difficult/subtle cases for each abnormality estimated the relative gains in accuracy (linear-scaled area below the ROC curve) obtained by averaging the case-ratings across (a) six independent replications by each reader (25% gain), (b) six different readers within each replication (34% gain), or (c) all 36 readings (48% gain). Although accuracy differed among both readers and abnormalities, ROC curves for the median ratings showed similar relative gains in accuracy, somewhat greater than those predicted from the measured rating correlations. A model for variance components in the observer's latent decision variable could predict these gains from measured correlations in the single ratings of cases. Depending on whether the model's estimates were based on realized accuracy gains or on rating correlations, about 48% or 39% of each reader's total decision variance (summed variance for positive and negative cases) consisted of random (within-reader) error that was uncorrelated between replications, another 10% or 14% came from idiosyncratic responses to individual cases, and about 43% or 47% was systematic variation that all readers found in the sampled cases.
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Affiliation(s)
- R G Swensson
- Department of Radiology, University of Pittsburgh, Pennsylvania 15261, USA.
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Abstract
PURPOSE To examine the combined effects of image resolution and display luminance on observer performance for detection of abnormalities depicted on posteroanterior chest radiographs. MATERIALS AND METHODS A total of 529 radiographs were displayed on a specially constructed view box at three luminance levels (770, 260, and 85 cd/m(2)) and three resolutions (100-microm, 200-microm, and 400-microm pixels). Each image was reviewed nine times by six radiologists who participated in this study. The abnormalities included nodule, pneumothorax, interstitial disease, alveolar infiltrates, and rib fracture. Negative (normal) radiographs were also included. RESULTS Receiver operating characteristic curves indicated that the effect of image luminance was greater than that of resolution. The detection of pneumothorax, interstitial disease, and rib fracture showed statistically significant differences (P <. 05) due to luminance. The detection of pneumothorax was the only abnormality with a statistically significant difference due to resolution. There was no evidence that luminance was related to image resolution for any of the abnormalities. CONCLUSION At a resolution of 400-microm pixels or higher across the field of view and a luminance of 260 cd/m(2) or more, primary diagnosis with posteroanterior chest radiographs is not likely to be affected by the quality of display.
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Affiliation(s)
- J M Herron
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA 15261-0001, USA
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Abstract
RATIONALE AND OBJECTIVES We performed a multipoint rank-order experiment to evaluate variability in observers' sensitivity to small differences in image presentation and to assess observers' performance as a function of the type and number of tasks included. METHODS Five experienced observers were presented with four sets of chest images that had been compressed at five different levels. Each set contained six images ranging from noncompressed to approximately 60:1-compressed images. Observers were asked to review all images of each case side by side and rank-order the "quality" of each to enable determination of the presence or absence of interstitial disease and/or pneumothoraces. RESULTS Observers varied significantly in their ability to detect very small differences among the images (P < 0.001). Those who performed well did so regardless of whether they ranked a specific abnormality in a multidisease or a single-disease setting. CONCLUSIONS Selected observers can reliably detect very small differences among similar images. These readers could be used to confirm or rule out the need for objective observer-performance-type studies.
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Affiliation(s)
- J D Towers
- Department of Radiology, University of Pittsburgh, Pennsylvania 15261-0001, USA
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Rockette HE, Campbell WL, Britton CA, Holbert JM, King JL, Gur D. Empiric assessment of parameters that affect the design of multireader receiver operating characteristic studies. Acad Radiol 1999; 6:723-9. [PMID: 10887893 DOI: 10.1016/s1076-6332(99)80468-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [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: 10/25/2022]
Abstract
RATIONALE AND OBJECTIVES The authors attempted to assess experimentally the magnitude of reader variability and the correlations and interactions among cases, readers, and modalities during observer performance studies and their possible effects on study design and sample size. MATERIALS AND METHODS Published data from 32 selected receiver operating characteristic (ROC) studies were reviewed to compare the magnitude of the variance component from readers with the variance component from modality. Estimates of correlation and interactions among cases, readers, and modalities were also computed directly from ROC data ascertained during two large studies performed in our laboratory. Each of these two studies included 529 cases and six readers, but one study used eight modalities and the other nine. RESULTS Published results indicate that reader variability is task dependent and larger (P < .05) than modality variability in detection of interstitial disease. Measured correlations between modalities for the same reader were task dependent and ranged from 0.35 to 0.59. Modality-by-reader and modality-by-case interactions often are not important factors. The random error term was greater than the modality-by-reader interaction in 11 of 20 comparisons and greater than the modality-by-case interaction in eight of 20 comparisons. CONCLUSION Use of the same cases interpreted with different modes is justifiable in many situations because of the high variability from readers. This comprehensive review of existing ROC studies resulted in parameter assessments that can be used to better estimate sample-size requirements in multireader ROC studies.
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Affiliation(s)
- H E Rockette
- Department of Biostatistics, University of Pittsburgh, PA 15261, USA
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