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Williams S, Hebblewhite M, Martin H, Meyer C, Whittington J, Killeen J, Berg J, MacAulay K, Smolko P, Merrill EH. Predation risk drives long-term shifts in migratory behaviour and demography in a large herbivore population. J Anim Ecol 2024; 93:21-35. [PMID: 37982331 DOI: 10.1111/1365-2656.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/27/2023] [Indexed: 11/21/2023]
Abstract
Migration is an adaptive life-history strategy across taxa that helps individuals maximise fitness by obtaining forage and avoiding predation risk. The mechanisms driving migratory changes are poorly understood, and links between migratory behaviour, space use, and demographic consequences are rare. Here, we use a nearly 20-year record of individual-based monitoring of a large herbivore, elk (Cervus canadensis) to test hypotheses for changing patterns of migration in and adjacent to a large protected area in Banff National Park (BNP), Canada. We test whether bottom-up (forage quality) or top-down (predation risk) factors explained trends in (i) the proportion of individuals using 5 different migratory tactics, (ii) differences in survival rates of migratory tactics during migration and whilst on summer ranges, (iii) cause-specific mortality by wolves and grizzly bears, and (iv) population abundance. We found dramatic shifts in migration consistent with behavioural plasticity in individual choice of annual migratory routes. Shifts were inconsistent with exposure to the bottom-up benefits of migration. Instead, exposure to landscape gradients in predation risk caused by exploitation outside the protected area drove migratory shifts. Carnivore exploitation outside the protected area led to higher survival rates for female elk remaining resident or migrating outside the protected area. Cause-specific mortality aligned with exposure to predation risk along migratory routes and summer ranges. Wolf predation risk was higher on migratory routes than summer ranges of montane-migrant tactics, but wolf predation risk traded-off with heightened risk from grizzly bears on summer ranges. A novel eastern migrant tactic emerged following a large forest fire that enhanced forage in an area with lower predation risk outside of the protected area. The changes in migratory behaviour translated to population abundance, where abundance of the montane-migratory tactics declined over time. The presence of diverse migratory life histories maintained a higher total population abundance than would have been the case with only one migratory tactic in the population. Our study demonstrates the complex ways in which migratory populations change over time through behavioural plasticity and associated demographic consequences because of individuals balancing predation risk and forage trade-offs.
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Affiliation(s)
- S Williams
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, Franke College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - M Hebblewhite
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, Franke College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - H Martin
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, Franke College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - C Meyer
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, Franke College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - J Whittington
- Banff National Park, Parks Canada, Banff, Alberta, Canada
| | - J Killeen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - J Berg
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - K MacAulay
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - P Smolko
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Applied Zoology and Wildlife Management, Technical University in Zvolen, Zvolen, Slovakia
| | - E H Merrill
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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2
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Sorensen SA, Gouwens NW, Wang Y, Mallory M, Budzillo A, Dalley R, Lee B, Gliko O, Kuo HC, Kuang X, Mann R, Ahmadinia L, Alfiler L, Baftizadeh F, Baker K, Bannick S, Bertagnolli D, Bickley K, Bohn P, Brown D, Bomben J, Brouner K, Chen C, Chen K, Chvilicek M, Collman F, Daigle T, Dawes T, de Frates R, Dee N, DePartee M, Egdorf T, El-Hifnawi L, Enstrom R, Esposito L, Farrell C, Gala R, Glomb A, Gamlin C, Gary A, Goldy J, Gu H, Hadley K, Hawrylycz M, Henry A, Hill D, Hirokawa KE, Huang Z, Johnson K, Juneau Z, Kebede S, Kim L, Lee C, Lesnar P, Li A, Glomb A, Li Y, Liang E, Link K, Maxwell M, McGraw M, McMillen DA, Mukora A, Ng L, Ochoa T, Oldre A, Park D, Pom CA, Popovich Z, Potekhina L, Rajanbabu R, Ransford S, Reding M, Ruiz A, Sandman D, Siverts L, Smith KA, Stoecklin M, Sulc J, Tieu M, Ting J, Trinh J, Vargas S, Vumbaco D, Walker M, Wang M, Wanner A, Waters J, Williams G, Wilson J, Xiong W, Lein E, Berg J, Kalmbach B, Yao S, Gong H, Luo Q, Ng L, Sümbül U, Jarsky T, Yao Z, Tasic B, Zeng H. Connecting single-cell transcriptomes to projectomes in mouse visual cortex. bioRxiv 2023:2023.11.25.568393. [PMID: 38168270 PMCID: PMC10760188 DOI: 10.1101/2023.11.25.568393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neuron's role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morpho-electric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.
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Affiliation(s)
| | | | - Yun Wang
- Allen Institute for Brain Science
| | | | | | | | | | | | | | - Xiuli Kuang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | | | - Chao Chen
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Kai Chen
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science
| | | | | | | | | | | | | | | | | | | | | | | | - Hong Gu
- Allen Institute for Brain Science
| | | | | | | | | | | | - Zili Huang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | - Lisa Kim
- Allen Institute for Brain Science
| | | | | | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | | | - Yaoyao Li
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | - Zoran Popovich
- University of Washington, Dept. of Computer Science and Engineering
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wei Xiong
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Ed Lein
- Allen Institute for Brain Science
| | - Jim Berg
- Allen Institute for Brain Science
| | | | | | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Qingming Luo
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Lydia Ng
- Allen Institute for Brain Science
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3
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Chartrand T, Dalley R, Close J, Goriounova NA, Lee BR, Mann R, Miller JA, Molnar G, Mukora A, Alfiler L, Baker K, Bakken TE, Berg J, Bertagnolli D, Braun T, Brouner K, Casper T, Csajbok EA, Dee N, Egdorf T, Enstrom R, Galakhova AA, Gary A, Gelfand E, Goldy J, Hadley K, Heistek TS, Hill D, Jorstad N, Kim L, Kocsis AK, Kruse L, Kunst M, Leon G, Long B, Mallory M, McGraw M, McMillen D, Melief EJ, Mihut N, Ng L, Nyhus J, Oláh G, Ozsvár A, Omstead V, Peterfi Z, Pom A, Potekhina L, Rajanbabu R, Rozsa M, Ruiz A, Sandle J, Sunkin SM, Szots I, Tieu M, Toth M, Trinh J, Vargas S, Vumbaco D, Williams G, Wilson J, Yao Z, Barzo P, Cobbs C, Ellenbogen RG, Esposito L, Ferreira M, Gouwens NW, Grannan B, Gwinn RP, Hauptman JS, Jarsky T, Keene CD, Ko AL, Koch C, Ojemann JG, Patel A, Ruzevick J, Silbergeld DL, Smith K, Sorensen SA, Tasic B, Ting JT, Waters J, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Kalmbach B, Lein ES. Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex. Science 2023; 382:eadf0805. [PMID: 37824667 DOI: 10.1126/science.adf0805] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 10/06/2022] [Accepted: 09/09/2023] [Indexed: 10/14/2023]
Abstract
Neocortical layer 1 (L1) is a site of convergence between pyramidal-neuron dendrites and feedback axons where local inhibitory signaling can profoundly shape cortical processing. Evolutionary expansion of human neocortex is marked by distinctive pyramidal neurons with extensive L1 branching, but whether L1 interneurons are similarly diverse is underexplored. Using Patch-seq recordings from human neurosurgical tissue, we identified four transcriptomic subclasses with mouse L1 homologs, along with distinct subtypes and types unmatched in mouse L1. Subclass and subtype comparisons showed stronger transcriptomic differences in human L1 and were correlated with strong morphoelectric variability along dimensions distinct from mouse L1 variability. Accompanied by greater layer thickness and other cytoarchitecture changes, these findings suggest that L1 has diverged in evolution, reflecting the demands of regulating the expanded human neocortical circuit.
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Affiliation(s)
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Natalia A Goriounova
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Gabor Molnar
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Eva Adrienn Csajbok
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Anna A Galakhova
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Tim S Heistek
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nik Jorstad
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Agnes Katalin Kocsis
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica J Melief
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Norbert Mihut
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gáspár Oláh
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Attila Ozsvár
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Zoltan Peterfi
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Alice Pom
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Marton Rozsa
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Joanna Sandle
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Ildiko Szots
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Martin Toth
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Sara Vargas
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Julia Wilson
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | | | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Benjamin Grannan
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Jason S Hauptman
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Jacob Ruzevick
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Christiaan P J de Kock
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Huib D Mansvelder
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Gabor Tamas
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
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4
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Lee BR, Dalley R, Miller JA, Chartrand T, Close J, Mann R, Mukora A, Ng L, Alfiler L, Baker K, Bertagnolli D, Brouner K, Casper T, Csajbok E, Donadio N, Driessens SLW, Egdorf T, Enstrom R, Galakhova AA, Gary A, Gelfand E, Goldy J, Hadley K, Heistek TS, Hill D, Hou WH, Johansen N, Jorstad N, Kim L, Kocsis AK, Kruse L, Kunst M, León G, Long B, Mallory M, Maxwell M, McGraw M, McMillen D, Melief EJ, Molnar G, Mortrud MT, Newman D, Nyhus J, Opitz-Araya X, Ozsvár A, Pham T, Pom A, Potekhina L, Rajanbabu R, Ruiz A, Sunkin SM, Szöts I, Taskin N, Thyagarajan B, Tieu M, Trinh J, Vargas S, Vumbaco D, Waleboer F, Walling-Bell S, Weed N, Williams G, Wilson J, Yao S, Zhou T, Barzó P, Bakken T, Cobbs C, Dee N, Ellenbogen RG, Esposito L, Ferreira M, Gouwens NW, Grannan B, Gwinn RP, Hauptman JS, Hodge R, Jarsky T, Keene CD, Ko AL, Korshoej AR, Levi BP, Meier K, Ojemann JG, Patel A, Ruzevick J, Silbergeld DL, Smith K, Sørensen JC, Waters J, Zeng H, Berg J, Capogna M, Goriounova NA, Kalmbach B, de Kock CPJ, Mansvelder HD, Sorensen SA, Tamas G, Lein ES, Ting JT. Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex. Science 2023; 382:eadf6484. [PMID: 37824669 DOI: 10.1126/science.adf6484] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 11/09/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Human cortex transcriptomic studies have revealed a hierarchical organization of γ-aminobutyric acid-producing (GABAergic) neurons from subclasses to a high diversity of more granular types. Rapid GABAergic neuron viral genetic labeling plus Patch-seq (patch-clamp electrophysiology plus single-cell RNA sequencing) sampling in human brain slices was used to reliably target and analyze GABAergic neuron subclasses and individual transcriptomic types. This characterization elucidated transitions between PVALB and SST subclasses, revealed morphological heterogeneity within an abundant transcriptomic type, identified multiple spatially distinct types of the primate-specialized double bouquet cells (DBCs), and shed light on cellular differences between homologous mouse and human neocortical GABAergic neuron types. These results highlight the importance of multimodal phenotypic characterization for refinement of emerging transcriptomic cell type taxonomies and for understanding conserved and specialized cellular properties of human brain cell types.
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Affiliation(s)
- Brian R Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Thomas Chartrand
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lauren Alfiler
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Eva Csajbok
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | | | - Stan L W Driessens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Enstrom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Emily Gelfand
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Dijon Hill
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wen-Hsien Hou
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | - Nik Jorstad
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Agnes Katalin Kocsis
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Michael Kunst
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Gabriela León
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Erica J Melief
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | | | - Dakota Newman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Attila Ozsvár
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | - Alice Pom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ram Rajanbabu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Augustin Ruiz
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ildikó Szöts
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jessica Trinh
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Sara Vargas
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Vumbaco
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | | | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Grace Williams
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julia Wilson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thomas Zhou
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Pál Barzó
- Department of Neurosurgery, University of Szeged, 6725 Szeged, Hungary
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Luke Esposito
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | | | - Benjamin Grannan
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Ryder P Gwinn
- Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jason S Hauptman
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Rebecca Hodge
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | | | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kaare Meier
- Department of Neurosurgery, Aarhus University Hospital, 8200 Aarhus, Denmark
- Department of Anesthesiology, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Anoop Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Jacob Ruzevick
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jens Christian Sørensen
- Department of Neurosurgery, Aarhus University Hospital, 8200 Aarhus, Denmark
- Center for Experimental Neuroscience, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Marco Capogna
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Huib D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | | | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
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5
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Kim MH, Radaelli C, Thomsen ER, Monet D, Chartrand T, Jorstad NL, Mahoney JT, Taormina MJ, Long B, Baker K, Bakken TE, Campagnola L, Casper T, Clark M, Dee N, D'Orazi F, Gamlin C, Kalmbach BE, Kebede S, Lee BR, Ng L, Trinh J, Cobbs C, Gwinn RP, Keene CD, Ko AL, Ojemann JG, Silbergeld DL, Sorensen SA, Berg J, Smith KA, Nicovich PR, Jarsky T, Zeng H, Ting JT, Levi BP, Lein E. Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex. eLife 2023; 12:e81863. [PMID: 37249212 PMCID: PMC10332811 DOI: 10.7554/elife.81863] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Rodent studies have demonstrated that synaptic dynamics from excitatory to inhibitory neuron types are often dependent on the target cell type. However, these target cell-specific properties have not been well investigated in human cortex, where there are major technical challenges in reliably obtaining healthy tissue, conducting multiple patch-clamp recordings on inhibitory cell types, and identifying those cell types. Here, we take advantage of newly developed methods for human neurosurgical tissue analysis with multiple patch-clamp recordings, post-hoc fluorescent in situ hybridization (FISH), machine learning-based cell type classification and prospective GABAergic AAV-based labeling to investigate synaptic properties between pyramidal neurons and PVALB- vs. SST-positive interneurons. We find that there are robust molecular differences in synapse-associated genes between these neuron types, and that individual presynaptic pyramidal neurons evoke postsynaptic responses with heterogeneous synaptic dynamics in different postsynaptic cell types. Using molecular identification with FISH and classifiers based on transcriptomically identified PVALB neurons analyzed by Patch-seq, we find that PVALB neurons typically show depressing synaptic characteristics, whereas other interneuron types including SST-positive neurons show facilitating characteristics. Together, these data support the existence of target cell-specific synaptic properties in human cortex that are similar to rodent, thereby indicating evolutionary conservation of local circuit connectivity motifs from excitatory to inhibitory neurons and their synaptic dynamics.
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Affiliation(s)
- Mean-Hwan Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Deja Monet
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | | | - Brian Long
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Tamara Casper
- Allen Institute for Brain ScienceSeattleUnited States
| | - Michael Clark
- Allen Institute for Brain ScienceSeattleUnited States
| | - Nick Dee
- Allen Institute for Brain ScienceSeattleUnited States
| | | | - Clare Gamlin
- Allen Institute for Brain ScienceSeattleUnited States
| | - Brian E Kalmbach
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology & Biophysics, School of Medicine, University of WashingtonSeattleUnited States
| | - Sara Kebede
- Allen Institute for Brain ScienceSeattleUnited States
| | - Brian R Lee
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lindsay Ng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jessica Trinh
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - C Dirk Keene
- Department of Laboratory Medicine & Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - Andrew L Ko
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | - Daniel L Silbergeld
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | | | - Jim Berg
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Tim Jarsky
- Allen Institute for Brain ScienceSeattleUnited States
| | - Hongkui Zeng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jonathan T Ting
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology & Biophysics, School of Medicine, University of WashingtonSeattleUnited States
| | - Boaz P Levi
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Laboratory Medicine & Pathology, School of Medicine, University of WashingtonSeattleUnited States
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
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6
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Gamlin CR, Schneider-Mizell CM, Mallory M, Elabbady L, Gouwens N, Williams G, Mukora A, Dalley R, Bodor A, Brittain D, Buchanan J, Bumbarger D, Kapner D, Kinn S, Mahalingam G, Seshamani S, Takeno M, Torres R, Yin W, Nicovich PR, Bae JA, Castro MA, Dorkenwald S, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Wong W, Wu J, Yu S, Berg J, Jarsky T, Lee B, Seung HS, Zeng H, Reid RC, Collman F, da Costa NM, Sorensen SA. Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types. bioRxiv 2023:2023.03.22.533857. [PMID: 36993629 PMCID: PMC10055412 DOI: 10.1101/2023.03.22.533857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Neural circuit function is shaped both by the cell types that comprise the circuit and the connections between those cell types 1 . Neural cell types have previously been defined by morphology 2, 3 , electrophysiology 4, 5 , transcriptomic expression 6-8 , connectivity 9-13 , or even a combination of such modalities 14-16 . More recently, the Patch-seq technique has enabled the characterization of morphology (M), electrophysiology (E), and transcriptomic (T) properties from individual cells 17-20 . Using this technique, these properties were integrated to define 28, inhibitory multimodal, MET-types in mouse primary visual cortex 21 . It is unknown how these MET-types connect within the broader cortical circuitry however. Here we show that we can predict the MET-type identity of inhibitory cells within a large-scale electron microscopy (EM) dataset and these MET-types have distinct ultrastructural features and synapse connectivity patterns. We found that EM Martinotti cells, a well defined morphological cell type 22, 23 known to be Somatostatin positive (Sst+) 24, 25 , were successfully predicted to belong to Sst+ MET-types. Each identified MET-type had distinct axon myelination patterns and synapsed onto specific excitatory targets. Our results demonstrate that morphological features can be used to link cell type identities across imaging modalities, which enables further comparison of connectivity in relation to transcriptomic or electrophysiological properties. Furthermore, our results show that MET-types have distinct connectivity patterns, supporting the use of MET-types and connectivity to meaningfully define cell types.
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7
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Buchin A, de Frates R, Nandi A, Mann R, Chong P, Ng L, Miller J, Hodge R, Kalmbach B, Bose S, Rutishauser U, McConoughey S, Lein E, Berg J, Sorensen S, Gwinn R, Koch C, Ting J, Anastassiou CA. Multi-modal characterization and simulation of human epileptic circuitry. Cell Rep 2022; 41:111873. [PMID: 36577383 PMCID: PMC9841067 DOI: 10.1016/j.celrep.2022.111873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/16/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
Temporal lobe epilepsy is the fourth most common neurological disorder, with about 40% of patients not responding to pharmacological treatment. Increased cellular loss is linked to disease severity and pathological phenotypes such as heightened seizure propensity. While the hippocampus is the target of therapeutic interventions, the impact of the disease at the cellular level remains unclear. Here, we show that hippocampal granule cells change with disease progression as measured in living, resected hippocampal tissue excised from patients with epilepsy. We show that granule cells increase excitability and shorten response latency while also enlarging in cellular volume and spine density. Single-nucleus RNA sequencing combined with simulations ascribes the changes to three conductances: BK, Cav2.2, and Kir2.1. In a network model, we show that these changes related to disease progression bring the circuit into a more excitable state, while reversing them produces a less excitable, "early-disease-like" state.
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Affiliation(s)
- Anatoly Buchin
- Allen Institute for Brain Science, Seattle, WA, USA,Present address: Cajal Neuroscience, Inc., Seattle, WA, USA,Correspondence: (A.B.), (C.A.A.)
| | - Rebecca de Frates
- Allen Institute for Brain Science, Seattle, WA, USA,These authors contributed equally
| | - Anirban Nandi
- Allen Institute for Brain Science, Seattle, WA, USA,These authors contributed equally
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA,University of Washington, Seattle, WA, USA
| | - Soumita Bose
- Allen Institute for Brain Science, Seattle, WA, USA,CiperHealth, San Francisco, CA, USA
| | - Ueli Rutishauser
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Center for Neural Science and Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stephen McConoughey
- Allen Institute for Brain Science, Seattle, WA, USA,Present address: Institute for Advanced Clinical Trials for Children, 9200 Corporate Blvd, Suite 350, Rockville, MD 20850, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA,University of Washington, Seattle, WA, USA
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jonathan Ting
- Allen Institute for Brain Science, Seattle, WA, USA,University of Washington, Seattle, WA, USA
| | - Costas A. Anastassiou
- Allen Institute for Brain Science, Seattle, WA, USA,Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Center for Neural Science and Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Lead contact,Correspondence: (A.B.), (C.A.A.)
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8
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Nandi A, Chartrand T, Van Geit W, Buchin A, Yao Z, Lee SY, Wei Y, Kalmbach B, Lee B, Lein E, Berg J, Sümbül U, Koch C, Tasic B, Anastassiou CA. Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types. Cell Rep 2022; 41:111659. [PMID: 36351398 PMCID: PMC9797078 DOI: 10.1016/j.celrep.2022.111659] [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: 11/09/2022] Open
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9
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Jablonowski R, Nordlund D, Xanthis C, Bidhult S, Kopic S, Berg J, Engblom H, Aletras AH, Arheden H. Longitudinal assessment of myocardial edema following experimental acute myocardial infarction using a comprehensive CMR protocol. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.350] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Preclinical and clinical data following acute myocardial infarction (MI) and reperfusion have shown a bimodal pattern of edematous myocardium at risk (MaR) on cardiovascular magnetic resonance (CMR) imaging during the first week [1,2]. In contrary, there have also been data demonstrating that MaR is stable during the first week in patients using contrast-enhanced steady-state free precession (CE-SSFP) imaging [3].
Purpose
To use a comprehensive CMR protocol to assess the dynamics of edematous MaR during the first week following acute experimental MI.
Methods
Acute myocardial ischemia was induced in seven pigs by endovascular balloon occlusion in the left anterior descending artery with reperfusion after 40 minutes. CMR was performed at baseline, at 120 minutes, 24 hours and seven days post-reperfusion on a 1.5T scanner. The CMR protocol comprised of a prototype T2-SSFP sequence where two experiments with 16 echo times (T2 mapping16) and with 10 echo times (T2 mapping10) [1] were performed. After contrast administration, a short-axis CE-SSFP stack and late gadolinium enhancement (LGE) images were acquired. T2-maps were acquired in a mid-apical ventricular short-axis slice corresponding to the same anatomical level at all time points. All image analysis was performed using designated software. Severity of MaR was measured by placing a region of interest in the ischemic area on T2 maps and extent of MaR was assessed by delineating hyperintense areas in CE-SSFP short-axis stacks. Data is presented as mean ± SD and one-way ANOVA was used followed by Tukey's multiple comparison test.
Results
An example of all acquired CMR sequences is shown in Figure 1, with red arrows depicting the extent of edematous MaR. Figure 2 shows the severity of MaR by T2 values from T2 mapping16 where T2 values were significantly lower at 24 hours compared to 120 minutes post-reperfusion (P<0.05). However, no significant difference was seen at 120 minutes or at 24 hours compared to T2 values at seven days (P=0.46 and P=0.35). No difference at baseline (47±3 ms vs 49±3 ms, P=0.10) was observed when comparing T2 mapping16 against T2 mapping10 but a significant difference between the time points 120 min (80±8 ms vs 69±7 ms, P=0.02), 24 h, (69±9 ms vs 54±4 ms, P=0.03), and seven days (76±10 ms vs 67±5 ms, P=0.04) post-reperfusion. There was no statistically significant difference between T2 values post-reperfusion using T2 mapping10 (P=ns). The extent of myocardium at risk assessed by CE-SSFP did not show a bimodal pattern of edema, but rather a significantly lower extent at seven days compared to the extent at 120 minutes and 24 hours (P<0.05).
Conclusion
The severity and extent of edematous myocardium at risk does not follow a bimodal pattern over the course of one week. However, absolute T2 values differ between T2 mapping sequences and therefore a standardization of a CMR protocol for the assessment of MaR is of importance.
Funding Acknowledgement
Type of funding sources: Foundation. Main funding source(s): The Swedish Heart-Lung Foundation and The Medical Faculty of Lund University (ALF)
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Affiliation(s)
- R Jablonowski
- Lund University, Skane University Hospital, Department of Clinical Physiology, Lund, Sweden , Lund , Sweden
| | - D Nordlund
- Lund University, Skane University Hospital, Department of Clinical Physiology, Lund, Sweden , Lund , Sweden
| | - C Xanthis
- Lund University, Skane University Hospital, Department of Clinical Physiology, Lund, Sweden , Lund , Sweden
| | - S Bidhult
- Lund University, Skane University Hospital, Department of Clinical Physiology, Lund, Sweden , Lund , Sweden
| | - S Kopic
- Lund University, Skane University Hospital, Department of Clinical Physiology, Lund, Sweden , Lund , Sweden
| | - J Berg
- Lund University, Skane University Hospital, Department of Clinical Physiology, Lund, Sweden , Lund , Sweden
| | - H Engblom
- Lund University, Skane University Hospital, Department of Clinical Physiology, Lund, Sweden , Lund , Sweden
| | - A H Aletras
- Aristotle University of Thessaloniki, Laboratory of Biomedical-Imaging Technologies, Aristotle University of Thessaloniki, Greece , Thessaloniki , Greece
| | - H Arheden
- Lund University, Skane University Hospital, Department of Clinical Physiology, Lund, Sweden , Lund , Sweden
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10
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Berg J, Villatore A, Sivilotti F, Pili G, Sala S, Della Bella P, Peretto G. Diagnostic value of electroanatomical mapping in patients with suspected arrhythmogenic cardiomyopathy. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.661] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Case series suggested that low voltage areas (LVA) on invasive electroanatomical mapping (EAM) could identify arrhythmogenic cardiomyopathy (ACM) at an earlier stage as compared to late gadolinium enhancement (LGE) and fatty infiltration on cardiac magnetic resonance (CMR). Data comparing LVA with structural abnormalities on CMR are lacking.
Purpose
To report the prevalence of substrate abnormalities identified by EAM vs. CMR in a cohort of patients with suspected ACM.
Methods
We retrospectively identified 66 consecutive patients with suspected ACM, who underwent EAM following clinical onset with ventricular arrhythmias. The cutoff value for EAM-defined LVA was <0.5 mV bipolar, <8 mV unipolar. Data from a prior CMR, performed no more than 12 months before, were used for comparison.
Results
The study cohort (mean age 47 years, range 21–76; 83% males; mean left ventricular ejection fraction 53%, range 28–70%) was composed of patients with suspected ACM involving either the right (n=62) or the left ventricle (n=4) following presentation with sustained monomorphic ventricular tachycardia. EAM was obtained by isolated endocardial, epicardial, or combined approach, respectively, in 11 (17%), 15 (23%) and 40 (61%) patients. Overall, 61 patients (92%) had documented LVA, of whom 89% showed an epicardial localization. In the same population, CMR identified a lower prevalence of substrate abnormalities (LGE 65%; fatty infiltration 50%). In particular, there were 27 patients (41%) with EAM-defined LVA and absent substrate abnormalities on CMR. Based on the 2010 Task Force Criteria and the 2021 Padua Criteria, a definite diagnosis of ACM was missing for a total of 19 patients (29%): due to the uniform identification of LVA in the absence of CMR abnormalities, EAM helped to establish the most likely diagnosis of ACM in all of them (19/19).
Conclusions
Our data suggest that EAM is capable of identifying substrate abnormalities in a consistent proportion of patients with suspected ACM and absent abnormalities on CMR. In this setting, the implementation of LVA to the current diagnostic criteria could improve the diagnostic yield for ACM.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- J Berg
- San Raffaele Hospital, Department of arrhythmology , Milan , Italy
| | - A Villatore
- San Raffaele Hospital, Department of arrhythmology , Milan , Italy
| | - F Sivilotti
- San Raffaele Hospital, Department of arrhythmology , Milan , Italy
| | - G Pili
- San Raffaele Hospital, Department of arrhythmology , Milan , Italy
| | - S Sala
- San Raffaele Hospital, Department of arrhythmology , Milan , Italy
| | - P Della Bella
- San Raffaele Hospital, Department of arrhythmology , Milan , Italy
| | - G Peretto
- San Raffaele Hospital, Department of arrhythmology , Milan , Italy
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11
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Sivilotti F, Villatore A, Berg J, Romano SC, Parciante A, Pili G, Fioravanti F, El Sawaf B, Sala S, Della Bella P, Peretto G. High prevalence of malignant ventricular arrhythmias in patients with early-stage left ventricular noncompaction. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.679] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Early-stage left ventricular non compaction (LVNC) is a nonischemic cardiomyopathy characterized with nondilated phenotype and unpredictable risk of malignant ventricular arrhythmias (MVA).
Purpose
To report the occurrence of MVA in patients with early-stage LVNC.
Methods
Consecutive patients (n=63) diagnosed with LVNC according to recognized criteria either on transthoracic echocardiogram or cardiac magnetic resonance were retrospectively enrolled. Patients with late-stage LVNC, defined by a coexistent dilated cardiomyopathy phenotype, were excluded (n=49). Patient-tailored medical treatment, as well as ICD implantation strategies, were based on the updated ESC guidelines integrated by the experience of a referral center for arrhythmia management. The study endpoint was the occurrence of MVA (defined as sustained VT, VF, or appropriate ICD therapy) by 5-year follow-up.
Results
The study cohort consisted of 14 patients (mean age 37±17 y, 64% males), presenting with palpitation (n=4), syncope (n=4), or dyspnea on effort (n=6). LVNC was diagnosed by echocardiogram and cardiac magnetic resonance in 13 and 1 patients, respectively. Because of nonmalignant VA, seven patients (50%) underwent ICD implant before discharge. By 5-year follow-up, 5 patients (36%) experienced MVA, including VF or appropriate ICD shocks for fast VT. Left ventricular ejection fraction (LVEF) ≥45% was the only factor associated with the occurrence of MVA (5/11 event in cases with LVEF ≥45% vs. 0/3 events in controls with LVEF <45%; p=0.145). Baseline features, including age, gender, NC/C ratio, and clinical presentation were comparable between cases with LVEF ≥45% and controls, all p>0.05. Drug treatment, including RAAS inhibitors, betablockers and antiarrhythmics was also comparable.
Conclusions
Our preliminary data show that in early-stage LVNC the occurrence of MVA is higher for patients with LVEF ≥45%. Efforts are needed to identify earlier predictors of arrhythmic risk, to improve patient selection for ICD implant.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- F Sivilotti
- University Vita-Salute San Raffaele , Milan , Italy
| | - A Villatore
- University Vita-Salute San Raffaele , Milan , Italy
| | - J Berg
- San Raffaele Hospital , Milan , Italy
| | - S C Romano
- University Vita-Salute San Raffaele , Milan , Italy
| | - A Parciante
- University Vita-Salute San Raffaele , Milan , Italy
| | - G Pili
- University Vita-Salute San Raffaele , Milan , Italy
| | | | | | - S Sala
- San Raffaele Hospital , Milan , Italy
| | | | - G Peretto
- San Raffaele Hospital , Milan , Italy
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12
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Berg J, Jablonowski R, Nordlund D, Ryd D, Heiberg E, Carlsson M, Arheden H. Hypothermia yields favourable cardiac energetics in experimental ischemia/reperfusion – insights from non-invasive pressure-volume loops by CMR. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2911] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background/Introduction
In experimental studies, mild hypothermia (<35°C) has reduced infarct size [1], potentially through reduced reperfusion injury [2], but human trials have been ambiguous [3]. Furthermore, a pressure-volume (PV) loop framework is the gold standard for assessing cardiac performance, but the invasive approach limits its clinical use. Therefore, we used a porcine model of ischemia/reperfusion with cardiovascular magnetic resonance (CMR) imaging throughout one week to acquire non-invasive PV loops.
Purpose
To quantify the cardioprotective effects of hypothermia at reperfusion by serial CMR imaging in a perspective of cardiac energy and mechanics.
Methods
Normothermia and Hypothermia groups (n=7+7 pigs) were imaged with CMR at baseline and subjected to 40 minutes of normothermic ischemia by catheter intervention. Thereafter, the Hypothermia group was rapidly cooled (<35°C) for 5 minutes before reperfusion. Additional imaging at two hours, 24 hours, and seven days were used to assess ventricular volumes and ischemic injuries. Infarct size was determined by high-resolution ex-vivo T1-weighted images.
Results
Figure 1 shows that stroke volume (SV: p=0.029; Friedmans test) and ejection fraction (EF: p=0.068) were notably reduced post-reperfusion in the Normothermia group. In contrast, the decreases were ameliorated in the Hypothermia group (SV: p=0.77; EF: p=0.13). Mean arterial pressure (MAP) was stable in the Normothermia group (p=0.77) but dropped two hours post-reperfusion in hypothermic animals (p=0.007). Over one week, both groups experienced the same decrease and partial recovery pattern for stroke work, external power, and ventricular-arterial coupling. Still, the adverse effects from ischemia were generally attenuated in the Hypothermia group. Although not significant, ischemia/reperfusion caused smaller infarcts in the Hypothermia group (10±8% vs 15±8%; p=0.32). The change in PV loop variables from baseline to 24 hours was compared with infarct size for each group. Though statistical power was limited, the general trend in analyses of covariance indicated that hypothermia has cardioprotective properties incremental to reducing infarct sizes (Figure 2), such as higher external power (p=0.061) and lower arterial elastance (p=0.015).
Conclusion
Using non-invasive PV loops by CMR, we observed that mild hypothermia before reperfusion results in favourable cardiac energetics that alleviates the heart's work after an ischemia/reperfusion injury during the first week. This study suggests that hypothermia has cardioprotective properties, incremental to reducing infarct size. The primary cardioprotective mechanism was likely an afterload reduction unloading the injured left ventricle.
Funding Acknowledgement
Type of funding sources: Foundation. Main funding source(s): The Swedish Heart-Lung FoundationThe Medical Faculty of Lund University (ALF)
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Affiliation(s)
- J Berg
- Lund University, Department of Clinical Sciences Lund, Clinical Physiology , Lund , Sweden
| | - R Jablonowski
- Lund University, Department of Clinical Sciences Lund, Clinical Physiology , Lund , Sweden
| | - D Nordlund
- Lund University, Department of Clinical Sciences Lund, Clinical Physiology , Lund , Sweden
| | - D Ryd
- Lund University, Department of Clinical Sciences Lund, Clinical Physiology , Lund , Sweden
| | - E Heiberg
- Lund University, Department of Clinical Sciences Lund, Clinical Physiology , Lund , Sweden
| | - M Carlsson
- National Institute of Health (Home), Laboratory of Clinical Physiology, National Heart Lung and Blood Institute, Washington , DC , United States of America
| | - H Arheden
- Lund University, Department of Clinical Sciences Lund, Clinical Physiology , Lund , Sweden
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13
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Loveday C, Garrett A, Law P, Hanks S, Poyastro-Pearson E, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Greenhalgh L, Henderson A, Izatt L, Kumar A, Lalloo F, Miedzybrodzka Z, Morrison PJ, Paterson J, Porteous M, Rogers MT, Walker L, Eccles D, Evans DG, Snape K, Hanson H, Houlston RS, Turnbull C. Analysis of rare disruptive germline mutations in 2,135 enriched BRCA-negative breast cancers excludes additional high-impact susceptibility genes. Ann Oncol 2022; 33:1318-1327. [PMID: 36122798 DOI: 10.1016/j.annonc.2022.09.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Breast cancer has a significant heritable basis, of which approximately 60% remains unexplained. Testing for BRCA1/BRCA2 offers useful discrimination of breast cancer risk within families, and identification of additional breast cancer susceptibility genes could offer clinical utility. PATIENTS AND METHODS We included 2,135 invasive breast cancer cases recruited via the BOCS study, a retrospective UK study of familial breast cancer. ELIGIBILITY CRITERIA female, BRCA-negative, white European ethnicity, and one of: i) breast cancer family history, ii) bilateral disease, iii) young age of onset (<30 years), iv) concomitant ovarian cancer. We undertook exome sequencing of cases and performed gene-level burden testing of rare damaging variants against those from 51,377 ethnicity-matched population controls from gnomAD. RESULTS 159/2135 (7.4%) cases had a qualifying variant in an established breast cancer susceptibility gene, with minimal evidence of signal in other cancer susceptibility genes. Known breast cancer susceptibility genes PALB2, CHEK2 and ATM were the only genes to retain statistical significance after correcting for multiple testing. Due to the enrichment of hereditary cases in the series, we had good power (>80%) to detect a gene of BRCA1-like risk (odds ratio = 10.6) down to a population minor allele frequency of 4.6 x 10-5 (1 in 10,799, less than one tenth that of BRCA1)and of PALB2-like risk (odds ratio = 5.0) down to a population minor allele frequency of 2.8 x 10-4 (1 in 1,779, less than half that of PALB2). Power was lower for identification of novel moderate penetrance genes (odds ratio = 2-3) like CHEK2 and ATM. CONCLUSIONS This is the largest case-control whole-exome analysis of enriched breast cancer published to date. Whilst additional breast cancer susceptibility genes likely exist, those of high penetrance are likely to be of very low mutational frequency. Contention exists regarding the clinical utility of such genes.
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Affiliation(s)
- C Loveday
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - A Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - P Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - S Hanks
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - E Poyastro-Pearson
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - J W Adlard
- Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, UK
| | - J Barwell
- Leicestershire Genetics Centre, University Hospitals of Leicester National Health Service (NHS) Trust, Leicester, UK
| | - J Berg
- Division of Medical Sciences, Human Genetics, University of Dundee, Dundee, UK
| | - A F Brady
- North West Thames Regional Genetics Service, Kennedy Galton Centre, London, UK
| | - C Brewer
- Peninsula Regional Genetics Service, Royal Devon & Exeter Hospital, Exeter, UK
| | - C Chapman
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham, UK
| | - J Cook
- Sheffield Regional Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - R Davidson
- West of Scotland Regional Genetics Service, Ferguson Smith Centre for Clinical Genetics, Glasgow, UK
| | - A Donaldson
- South Western Regional Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol, UK
| | - F Douglas
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - L Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - A Henderson
- Northern Genetics Service (Cumbria), Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - L Izatt
- South East Thames Regional Genetics Service, Guy's and St. Thomas NHS Foundation Trust, London, UK
| | - A Kumar
- North East Thames Regional Genetics Service, Great Ormond St. Hospital, London, UK
| | - F Lalloo
- University Department of Medical Genetics & Regional Genetics Service, St. Mary's Hospital, Manchester, UK
| | - Z Miedzybrodzka
- University of Aberdeen and North of Scotland Clinical Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - P J Morrison
- Belfast Health and Social Care (HSC) Trust & Department of Medical Genetics, Northern Ireland Regional Genetics Service, Queen's University Belfast, Belfast, UK
| | - J Paterson
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - M Porteous
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, UK
| | - M T Rogers
- All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, UK
| | - L Walker
- Oxford Regional Genetics Service, Oxford Radcliffe Hospitals NHS Trust, Oxford, UK
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- Individual collaborators and their affiliations are listed in the Appendix
| | - D Eccles
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton, UK
| | - D G Evans
- University Department of Medical Genetics & Regional Genetics Service, St. Mary's Hospital, Manchester, UK
| | - K Snape
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; South West Thames Regional Genetics Service, St. George's Hospital, London, UK
| | - H Hanson
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; South West Thames Regional Genetics Service, St. George's Hospital, London, UK
| | - R S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - C Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; Royal Marsden NHS Foundation Hospital, London, UK.
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14
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Nandi A, Chartrand T, Van Geit W, Buchin A, Yao Z, Lee SY, Wei Y, Kalmbach B, Lee B, Lein E, Berg J, Sümbül U, Koch C, Tasic B, Anastassiou CA. Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types. Cell Rep 2022; 40:111176. [PMID: 35947954 PMCID: PMC9793758 DOI: 10.1016/j.celrep.2022.111176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 01/28/2022] [Accepted: 07/18/2022] [Indexed: 12/30/2022] Open
Abstract
Which cell types constitute brain circuits is a fundamental question, but establishing the correspondence across cellular data modalities is challenging. Bio-realistic models allow probing cause-and-effect and linking seemingly disparate modalities. Here, we introduce a computational optimization workflow to generate 9,200 single-neuron models with active conductances. These models are based on 230 in vitro electrophysiological experiments followed by morphological reconstruction from the mouse visual cortex. We show that, in contrast to current belief, the generated models are robust representations of individual experiments and cortical cell types as defined via cellular electrophysiology or transcriptomics. Next, we show that differences in specific conductances predicted from the models reflect differences in gene expression supported by single-cell transcriptomics. The differences in model conductances, in turn, explain electrophysiological differences observed between the cortical subclasses. Our computational effort reconciles single-cell modalities that define cell types and enables causal relationships to be examined.
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Affiliation(s)
- Anirban Nandi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thomas Chartrand
- Allen Institute for Brain Science, Seattle, WA 98109, USA,These authors contributed equally
| | - Werner Van Geit
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, Geneva 1202, Switzerland,These authors contributed equally
| | - Anatoly Buchin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Soo Yeun Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Yina Wei
- Allen Institute for Brain Science, Seattle, WA 98109, USA,Zhejiang Lab, Hangzhou City, Zhejiang Province 311121, China
| | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Brian Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Uygar Sümbül
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Costas A. Anastassiou
- Allen Institute for Brain Science, Seattle, WA 98109, USA,Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Center for Neural Science and Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Lead contact,Correspondence:
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15
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Varpula J, Välimäki M, Lantta T, Berg J, Soininen P, Lahti M. Safety hazards in clinical practice of seclusion in psychiatric care. Eur Psychiatry 2022. [PMCID: PMC9566598 DOI: 10.1192/j.eurpsy.2022.708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Introduction Seclusion is part of the clinical practice in European psychiatric hospital care with the aim to maintain the safety of patients and staff. Adverse events and harm have been reported for patients and staff resulting from seclusion. Safety hazards, which are the prerequisite of adverse events, can be identified using video observation methods. Identifying safety hazards can be used to prevent adverse events and improve the quality of psychiatric care. Objectives To identify safety hazards during seclusion in psychiatric hospital care. Methods Descriptive design with non-participant video-observation of seclusion care practice. Data consisted of video recordings (n = 36) from six wards of one psychiatric hospital in Finland. The data were analysed with inductive thematic analysis. Results Clinical practice of seclusion included safety hazards stemming from the actions of patients and staff. Patients’ actions were as follows: aggressive behaviour, attempting to escape, precarious movements, preventing the visibility of staff, exposing themselves to contamination, and falls during seclusion. Staff actions included: leaving dangerous items to seclusion, issues in the administration of medication, performing physical and mechanical restraints in unsecure way, and precarious movements and postures. Conclusions According to our results, the use of seclusion has safety hazards that can result in harm for patients and staff. To improve the quality and safety of seclusion in clinical practice, the guidelines, practices, and staff training need to consider the various safety hazards. While the work in Europe to abolish the use of seclusion is still in progress, this topic requires attention in clinical practice, education, and policymaking. Disclosure No significant relationships.
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16
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Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Author Correction: Human neocortical expansion involves glutamatergic neuron diversification. Nature 2022; 601:E12. [PMID: 34992294 PMCID: PMC8770134 DOI: 10.1038/s41586-021-04322-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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Wendin K, Berg J, Jönsson K, Andersson P, Birch K, Davidsson F, Gerberich J, Rask S, Langton M. Introducing mealworm as an ingredient in crisps and pâtés – sensory characterization and consumer liking. Future Foods 2021. [DOI: 10.1016/j.fufo.2021.100082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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18
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Berg J, Jablonowski R, Mohammad M, Solem K, Borgquist R, Ostenfeld E, Arheden H, Carlsson M. Ventricular longitudinal shortening is an independent predictor of death in heart failure patients with reduced ejection fraction. Sci Rep 2021; 11:20280. [PMID: 34645886 PMCID: PMC8514526 DOI: 10.1038/s41598-021-99613-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/14/2021] [Indexed: 01/07/2023] Open
Abstract
Reduced ventricular longitudinal shortening measured by atrioventricular plane displacement (AVPD) and global longitudinal strain (GLS) are prognostic markers in heart disease. This study aims to determine if AVPD and GLS with cardiovascular magnetic resonance (CMR) are independent predictors of cardiovascular (CV) and all-cause death also in heart failure with reduced ejection fraction (HFrEF). Patients (n = 287) were examined with CMR and AVPD, GLS, ventricular volumes, myocardial fibrosis/scar were measured. Follow-up was 5 years with cause of death retrieved from a national registry. Forty CV and 60 all-cause deaths occurred and CV non-survivors had a lower AVPD (6.4 ± 2.0 vs 8.0 ± 2.4 mm, p < 0.001) and worse GLS (− 6.1 ± 2.2 vs − 7.7 ± 3.1%, p = 0.001). Kaplan–Meier analyses displayed increased survival for patients in the highest AVPD- and GLS-tertiles vs. the lowest tertiles (AVPD: p = 0.001, GLS: p = 0.013). AVPD and GLS showed in univariate analysis a hazard ratio (HR) of 1.30 (per-mm-decrease) and 1.19 (per-%-decrease) for CV death. Mean AVPD and GLS were independent predictors of all-cause death (HR = 1.24 per-mm-decrease and 1.15 per-%-decrease), but only AVPD showed incremental value over age, sex, body-mass-index, EF, etiology and fibrosis/scar for CV death (HR = 1.33 per-mm-decrease, p < 0.001). Ventricular longitudinal shortening remains independently prognostic for death in HFrEF even after adjusting for well-known clinical risk factors.
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Affiliation(s)
- J Berg
- Clinical Physiology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden.,Syntach AB, Lund, Sweden
| | - R Jablonowski
- Clinical Physiology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - M Mohammad
- Clinical Physiology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | | | - R Borgquist
- Cardiology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - E Ostenfeld
- Clinical Physiology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - H Arheden
- Clinical Physiology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - M Carlsson
- Clinical Physiology, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden.
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19
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Callaway EM, Dong HW, Ecker JR, Hawrylycz MJ, Huang ZJ, Lein ES, Ngai J, Osten P, Ren B, Tolias AS, White O, Zeng H, Zhuang X, Ascoli GA, Behrens MM, Chun J, Feng G, Gee JC, Ghosh SS, Halchenko YO, Hertzano R, Lim BK, Martone ME, Ng L, Pachter L, Ropelewski AJ, Tickle TL, Yang XW, Zhang K, Bakken TE, Berens P, Daigle TL, Harris JA, Jorstad NL, Kalmbach BE, Kobak D, Li YE, Liu H, Matho KS, Mukamel EA, Naeemi M, Scala F, Tan P, Ting JT, Xie F, Zhang M, Zhang Z, Zhou J, Zingg B, Armand E, Yao Z, Bertagnolli D, Casper T, Crichton K, Dee N, Diep D, Ding SL, Dong W, Dougherty EL, Fong O, Goldman M, Goldy J, Hodge RD, Hu L, Keene CD, Krienen FM, Kroll M, Lake BB, Lathia K, Linnarsson S, Liu CS, Macosko EZ, McCarroll SA, McMillen D, Nadaf NM, Nguyen TN, Palmer CR, Pham T, Plongthongkum N, Reed NM, Regev A, Rimorin C, Romanow WJ, Savoia S, Siletti K, Smith K, Sulc J, Tasic B, Tieu M, Torkelson A, Tung H, van Velthoven CTJ, Vanderburg CR, Yanny AM, Fang R, Hou X, Lucero JD, Osteen JK, Pinto-Duarte A, Poirion O, Preissl S, Wang X, Aldridge AI, Bartlett A, Boggeman L, O’Connor C, Castanon RG, Chen H, Fitzpatrick C, Luo C, Nery JR, Nunn M, Rivkin AC, Tian W, Dominguez B, Ito-Cole T, Jacobs M, Jin X, Lee CT, Lee KF, Miyazaki PA, Pang Y, Rashid M, Smith JB, Vu M, Williams E, Biancalani T, Booeshaghi AS, Crow M, Dudoit S, Fischer S, Gillis J, Hu Q, Kharchenko PV, Niu SY, Ntranos V, Purdom E, Risso D, de Bézieux HR, Somasundaram S, Street K, Svensson V, Vaishnav ED, Van den Berge K, Welch JD, An X, Bateup HS, Bowman I, Chance RK, Foster NN, Galbavy W, Gong H, Gou L, Hatfield JT, Hintiryan H, Hirokawa KE, Kim G, Kramer DJ, Li A, Li X, Luo Q, Muñoz-Castañeda R, Stafford DA, Feng Z, Jia X, Jiang S, Jiang T, Kuang X, Larsen R, Lesnar P, Li Y, Li Y, Liu L, Peng H, Qu L, Ren M, Ruan Z, Shen E, Song Y, Wakeman W, Wang P, Wang Y, Wang Y, Yin L, Yuan J, Zhao S, Zhao X, Narasimhan A, Palaniswamy R, Banerjee S, Ding L, Huilgol D, Huo B, Kuo HC, Laturnus S, Li X, Mitra PP, Mizrachi J, Wang Q, Xie P, Xiong F, Yu Y, Eichhorn SW, Berg J, Bernabucci M, Bernaerts Y, Cadwell CR, Castro JR, Dalley R, Hartmanis L, Horwitz GD, Jiang X, Ko AL, Miranda E, Mulherkar S, Nicovich PR, Owen SF, Sandberg R, Sorensen SA, Tan ZH, Allen S, Hockemeyer D, Lee AY, Veldman MB, Adkins RS, Ament SA, Bravo HC, Carter R, Chatterjee A, Colantuoni C, Crabtree J, Creasy H, Felix V, Giglio M, Herb BR, Kancherla J, Mahurkar A, McCracken C, Nickel L, Olley D, Orvis J, Schor M, Hood G, Dichter B, Grauer M, Helba B, Bandrowski A, Barkas N, Carlin B, D’Orazi FD, Degatano K, Gillespie TH, Khajouei F, Konwar K, Thompson C, Kelly K, Mok S, Sunkin S. A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 2021; 598:86-102. [PMID: 34616075 PMCID: PMC8494634 DOI: 10.1038/s41586-021-03950-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 08/25/2021] [Indexed: 12/14/2022]
Abstract
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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20
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Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Human neocortical expansion involves glutamatergic neuron diversification. Nature 2021; 598:151-158. [PMID: 34616067 PMCID: PMC8494638 DOI: 10.1038/s41586-021-03813-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [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] [Received: 04/01/2020] [Accepted: 07/07/2021] [Indexed: 11/09/2022]
Abstract
The neocortex is disproportionately expanded in human compared with mouse1,2, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers composed of neurons that selectively make connections within the neocortex and with other telencephalic structures. Single-cell transcriptomic analyses of human and mouse neocortex show an increased diversity of glutamatergic neuron types in supragranular layers in human neocortex and pronounced gradients as a function of cortical depth3. Here, to probe the functional and anatomical correlates of this transcriptomic diversity, we developed a robust platform combining patch clamp recording, biocytin staining and single-cell RNA-sequencing (Patch-seq) to examine neurosurgically resected human tissues. We demonstrate a strong correspondence between morphological, physiological and transcriptomic phenotypes of five human glutamatergic supragranular neuron types. These were enriched in but not restricted to layers, with one type varying continuously in all phenotypes across layers 2 and 3. The deep portion of layer 3 contained highly distinctive cell types, two of which express a neurofilament protein that labels long-range projection neurons in primates that are selectively depleted in Alzheimer's disease4,5. Together, these results demonstrate the explanatory power of transcriptomic cell-type classification, provide a structural underpinning for increased complexity of cortical function in humans, and implicate discrete transcriptomic neuron types as selectively vulnerable in disease.
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Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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21
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Lee BR, Budzillo A, Hadley K, Miller JA, Jarsky T, Baker K, Hill D, Kim L, Mann R, Ng L, Oldre A, Rajanbabu R, Trinh J, Vargas S, Braun T, Dalley RA, Gouwens NW, Kalmbach BE, Kim TK, Smith KA, Soler-Llavina G, Sorensen S, Tasic B, Ting JT, Lein E, Zeng H, Murphy GJ, Berg J. Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization. eLife 2021; 10:e65482. [PMID: 34387544 PMCID: PMC8428855 DOI: 10.7554/elife.65482] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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] [Received: 12/06/2020] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
The Patch-seq approach is a powerful variation of the patch-clamp technique that allows for the combined electrophysiological, morphological, and transcriptomic characterization of individual neurons. To generate Patch-seq datasets at scale, we identified and refined key factors that contribute to the efficient collection of high-quality data. We developed patch-clamp electrophysiology software with analysis functions specifically designed to automate acquisition with online quality control. We recognized the importance of extracting the nucleus for transcriptomic success and maximizing membrane integrity during nucleus extraction for morphology success. The protocol is generalizable to different species and brain regions, as demonstrated by capturing multimodal data from human and macaque brain slices. The protocol, analysis and acquisition software are compiled at https://githubcom/AllenInstitute/patchseqtools. This resource can be used by individual labs to generate data across diverse mammalian species and that is compatible with large publicly available Patch-seq datasets.
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Affiliation(s)
- Brian R Lee
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Tim Jarsky
- Allen Institute for Brain ScienceSeattleUnited States
| | | | - DiJon Hill
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lisa Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | - Rusty Mann
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lindsay Ng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Aaron Oldre
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ram Rajanbabu
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jessica Trinh
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sara Vargas
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Brian E Kalmbach
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Tae Kyung Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | | | - Jonathan T Ting
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Hongkui Zeng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Gabe J Murphy
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Jim Berg
- Allen Institute for Brain ScienceSeattleUnited States
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22
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Dudok B, Klein PM, Hwaun E, Lee BR, Yao Z, Fong O, Bowler JC, Terada S, Sparks FT, Szabo GG, Farrell JS, Berg J, Daigle TL, Tasic B, Dimidschstein J, Fishell G, Losonczy A, Zeng H, Soltesz I. Alternating sources of perisomatic inhibition during behavior. Neuron 2021; 109:997-1012.e9. [PMID: 33529646 PMCID: PMC7979482 DOI: 10.1016/j.neuron.2021.01.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 12/30/2022]
Abstract
Interneurons expressing cholecystokinin (CCK) and parvalbumin (PV) constitute two key GABAergic controllers of hippocampal pyramidal cell output. Although the temporally precise and millisecond-scale inhibitory regulation of neuronal ensembles delivered by PV interneurons is well established, the in vivo recruitment patterns of CCK-expressing basket cell (BC) populations has remained unknown. We show in the CA1 of the mouse hippocampus that the activity of CCK BCs inversely scales with both PV and pyramidal cell activity at the behaviorally relevant timescales of seconds. Intervention experiments indicated that the inverse coupling of CCK and PV GABAergic systems arises through a mechanism involving powerful inhibitory control of CCK BCs by PV cells. The tightly coupled complementarity of two key microcircuit regulatory modules demonstrates a novel form of brain-state-specific segregation of inhibition during spontaneous behavior.
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Affiliation(s)
- Barna Dudok
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA.
| | - Peter M Klein
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Ernie Hwaun
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - John C Bowler
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Satoshi Terada
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Fraser T Sparks
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Gergely G Szabo
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Jordan S Farrell
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tanya L Daigle
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jordane Dimidschstein
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gord Fishell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY 10027, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
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23
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Packer RA, Wachowiak I, Thomovsky SA, Berg J, Vasquez L, O'Brien DP. Phenotypic characterization of PIGN-associated paroxysmal dyskinesia in Soft-coated wheaten terriers and preliminary response to acetazolamide therapy. Vet J 2021; 269:105606. [PMID: 33593494 DOI: 10.1016/j.tvjl.2021.105606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 10/22/2022]
Abstract
A hereditary movement disorder in Soft coated wheaten terriers (SCWT) has been associated with a mutation in PIGN which encodes an enzyme involved in synthesis of glycosylphosphatidylinositol (GPI). The objective of this study was to describe and classify the clinical phenotype and assess therapeutic response. Twenty-five SCWT and related dogs homozygous for PIGN:c.398C>T with paroxysmal dyskinesia were available for inclusion. Medical records and video recordings of 17 dogs were evaluated in a retrospective case series. Affected dogs had episodes of involuntary, hyperkinetic movements and dystonia. Median age of onset was 2.5 years. A typical episode consisted of rapid, irregular hyperflexion and extension of the pelvic limbs with some degree of truncal dystonia. A mild episode consisted of spontaneous flexion of one pelvic limb while walking which could resemble a lameness. Episodes lasted several minutes to several hours and occurred up to 10 times/day or more. They were not associated with exercise or fasting but were sometimes triggered by excitement or stress. Acetazolamide therapy improved nine of 11 dogs, in seven cases abolishing episodes. Five of 17 dogs treated with other agents had mild improvement with clonazepam (n = 2), levetiracetam (n = 1), or phenobarbital (n = 2). Paroxysmal dyskinesias must be differentiated from seizure disorders since they often respond to different therapies. The SCWT phenotype consisted predominantly of hyperkinesia, and can respond dramatically to acetazolamide. GPI anchors proteins to the cell surface including carbonic anhydrase IV which modulates synaptic pH in the brain. Altered activity of this enzyme may be the target of acetazolamide therapy.
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Affiliation(s)
- R A Packer
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA.
| | - I Wachowiak
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - S A Thomovsky
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, Indiana, USA
| | - J Berg
- Animal Specialty Center, Yonkers, New York, USA
| | - L Vasquez
- Gulf Coast Veterinary Neurology and Neurosurgery, Houston, Texas, USA
| | - D P O'Brien
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
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24
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Steck O, Bertschi N, Luther F, Berg J, Winkel D, Holbro A, Schlapbach C. Rapid and sustained control of itch and reduction in Th2 bias by dupilumab in a patient with Sézary syndrome. J Eur Acad Dermatol Venereol 2020; 35:1331-1337. [DOI: 10.1111/jdv.17001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/05/2020] [Indexed: 12/22/2022]
Affiliation(s)
- O. Steck
- Department of Dermatology, Inselspital Bern University HospitalUniversity of Bern Bern Switzerland
| | - N.L. Bertschi
- Department of Dermatology, Inselspital Bern University HospitalUniversity of Bern Bern Switzerland
| | - F. Luther
- Department of Dermatology, Inselspital Bern University HospitalUniversity of Bern Bern Switzerland
| | - J. Berg
- Department of Hematology University Hospital Basel Basel Switzerland
- Blood Transfusion Center Swiss Red Cross Basel Switzerland
| | - D.J. Winkel
- Radiology & Nuclear Medicine Clinic University Hospital Basel Basel Switzerland
| | - A. Holbro
- Department of Hematology University Hospital Basel Basel Switzerland
- Blood Transfusion Center Swiss Red Cross Basel Switzerland
| | - C. Schlapbach
- Department of Dermatology, Inselspital Bern University HospitalUniversity of Bern Bern Switzerland
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25
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Gouwens NW, Sorensen SA, Baftizadeh F, Budzillo A, Lee BR, Jarsky T, Alfiler L, Baker K, Barkan E, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Crichton K, Daigle TL, Dalley R, de Frates RA, Dee N, Desta T, Lee SD, Dotson N, Egdorf T, Ellingwood L, Enstrom R, Esposito L, Farrell C, Feng D, Fong O, Gala R, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Graybuck L, Gu H, Hadley K, Hawrylycz MJ, Henry AM, Hill D, Hupp M, Kebede S, Kim TK, Kim L, Kroll M, Lee C, Link KE, Mallory M, Mann R, Maxwell M, McGraw M, McMillen D, Mukora A, Ng L, Ng L, Ngo K, Nicovich PR, Oldre A, Park D, Peng H, Penn O, Pham T, Pom A, Popović Z, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Robertson M, Ronellenfitch K, Ruiz A, Sandman D, Smith K, Sulc J, Sunkin SM, Szafer A, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Ward K, Williams G, Zhou Z, Ting JT, Arkhipov A, Sümbül U, Lein ES, Koch C, Yao Z, Tasic B, Berg J, Murphy GJ, Zeng H. Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells. Cell 2020; 183:935-953.e19. [PMID: 33186530 PMCID: PMC7781065 DOI: 10.1016/j.cell.2020.09.057] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/06/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022]
Abstract
Neurons are frequently classified into distinct types on the basis of structural, physiological, or genetic attributes. To better constrain the definition of neuronal cell types, we characterized the transcriptomes and intrinsic physiological properties of over 4,200 mouse visual cortical GABAergic interneurons and reconstructed the local morphologies of 517 of those neurons. We find that most transcriptomic types (t-types) occupy specific laminar positions within visual cortex, and, for most types, the cells mapping to a t-type exhibit consistent electrophysiological and morphological properties. These properties display both discrete and continuous variation among t-types. Through multimodal integrated analysis, we define 28 met-types that have congruent morphological, electrophysiological, and transcriptomic properties and robust mutual predictability. We identify layer-specific axon innervation pattern as a defining feature distinguishing different met-types. These met-types represent a unified definition of cortical GABAergic interneuron types, providing a systematic framework to capture existing knowledge and bridge future analyses across different modalities.
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Affiliation(s)
| | | | | | - Agata Budzillo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lauren Alfiler
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jasmine Bomben
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thomas Braun
- Byte Physics, Schwarzastraße 9, Berlin 12055, Germany
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Tanya L Daigle
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Rachel Enstrom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Luke Esposito
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Colin Farrell
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rohan Gala
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Melissa Gorham
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lucas Graybuck
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tae Kyung Kim
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Matthew Kroll
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hanchuan Peng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Osnat Penn
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Alice Pom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zoran Popović
- Center for Game Science, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | | | | | - Shea Ransford
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Reid
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Augustin Ruiz
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jessica Trinh
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Grace Williams
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zhi Zhou
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Anton Arkhipov
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Uygar Sümbül
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
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Patriki D, Baltensperger N, Berg J, Cooper LT, Kissel CK, Kottwitz J, Lovrinovic M, Manka R, Scherff F, Schmied C, Tanner FC, Luescher TF, Heidecker B. A Prospective Pilot Study to Identify a Myocarditis Cohort who may Safely Resume Sports Activities 3 Months after Diagnosis. J Cardiovasc Transl Res 2020; 14:670-673. [PMID: 32367345 PMCID: PMC8397673 DOI: 10.1007/s12265-020-09983-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022]
Abstract
International cardiovascular society recommendations to return to sports activities following acute myocarditis are based on expert consensus in the absence of prospective studies. We prospectively enrolled 30 patients with newly diagnosed myocarditis based on clinical parameters, laboratory measurements and cardiac magnetic resonance imaging with mildly reduced or preserved left ventricular ejection fraction (LVEF) with a follow-up of 12 months. Cessation of physical activity was recommended for 3 months. The average age was 35 (19-80) years with 73% male patients. One case of non-sustained ventricular tachycardia was recorded during 48-h-Holter electrocardiogram. Except for this case, all patients were allowed to resume physical exercise after 3 months. At 6- (n = 26) and 12-month (n = 19) follow-up neither cardiac events nor worsening LVEF were recorded. The risk of cardiac events at 1 year after diagnosis of myocarditis appears to be low after resumption of exercise after 3 months among patients who recover from acute myocarditis.
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Affiliation(s)
- D Patriki
- Cardiology, University Heart Center, Zurich, Switzerland
| | | | - J Berg
- Cardiology, University Heart Center, Zurich, Switzerland
| | | | - C K Kissel
- Cardiology, University Heart Center, Zurich, Switzerland
| | - J Kottwitz
- Cardiology, University Heart Center, Zurich, Switzerland
| | - M Lovrinovic
- Cardiology, University Heart Center, Zurich, Switzerland
| | - R Manka
- Cardiology, University Heart Center, Zurich, Switzerland
| | - F Scherff
- Cardiology, University Heart Center, Zurich, Switzerland
| | - C Schmied
- Cardiology, University Heart Center, Zurich, Switzerland
| | - F C Tanner
- Cardiology, University Heart Center, Zurich, Switzerland
| | - T F Luescher
- Center for Molecular Cardiology, University of Zurich, Zurich, Switzerland.,Imperial College and Royal Brompton & Harefield Hospital, London, UK
| | - Bettina Heidecker
- Cardiology, University Heart Center, Zurich, Switzerland. .,Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Germany, Hindenburgdamm 30, 12203, Berlin, Germany.
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27
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Berg J, Bonduelle Y, Golinval O. [Epithelioid trophoblastic tumour with pulmonary metastasis]. Rev Med Liege 2020; 75:145-150. [PMID: 32157837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Epithelioid trophoblastic tumours are rare kind of gestational trophoblastic disease. Their detection is made by repetitive measurement of ?HCG after any gestational period (including spontaneous abortion). Epithelioid trophoblastic tumour can cause pulmonary metastasis. We describe the clinical case of a 44-year old woman with a cystic lesion of the right pulmonary apex following a miscarriage which was an epithelioid trophoblastic tumour. She's still in complete remission after surgery and careful follow up.
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Affiliation(s)
- J Berg
- Service de Pneumologie, CHR Verviers, Belgique
| | - Y Bonduelle
- Service de Pneumologie, CHR Verviers, Belgique
| | - O Golinval
- Service de Pneumologie, CHR Verviers, Belgique
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Abstract
OBJECTIVES To determine the relationship between plant food consumption and bone mineral density (BMD) in a healthy population when age, gender, BMI and physical activity are accounted for. DESIGN Cross-sectional study. SETTING Participants were recruited from the Sydney Adventist hospital and the University of New South Wales, Sydney, Australia. PARTICIPANTS 33 males and 40 females (total n=73) participated in this study. The mean age was 56.1 ± 8.5 years. All participants were non-diabetic and in general good health. MEASUREMENTS A principle component analysis (PCA) was performed on 12 month self-report food intake data, gathered using the Cancer Council Victoria Dietary Questionnaire for Epidemiological Studies Version 2. Dual-energy X-ray absorptiometry was used to measure total BMD. Fasting plasma total protein, calcium and 25-Hydroxy Vitamin D levels were analysed by the Sydney Adventist Hospital pathology laboratory. Anthropometric measures were obtained using a standardized protocol. Self-reported physical activity levels were assessed using the International Physical Activity Questionnaire. RESULTS The PCA revealed three principle components. These were termed 'Meat Based', 'Junk Food' and 'Plant Based.' After controlling for age, gender, physical activity and BMI, the Plant Based component correlated positively with BMD (p=0.054, R2=0.439) and T-score (p=0.053, R2=0.221). Using a similar model no association between the Meat Based component and BMD or T-score was found. However, when the Plant Based component was included the Meat Based component correlated positively with BMD (p=0.046, R2=0.474) and T-score (p=0.046, R2=0.279). There was no significant association between the Junk Food component and BMD or T-score. People in the third Plant (927 ± 339 vs 751 ± 255 g/day, p=0.025) and Meat Based (921 ± 270 vs 676 ± 241 g/day, p=0.002) tertile had higher calcium intakes than those in the first. People in the second Plant Based tertile had higher plasma Vitamin D levels than those in the first (63.5 ± 16.8 vs. 52.3 ± 22.1 nmol/L, p=0.053) while those in the third Junk Food tertile had lower levels than those in the first (52.4 ± 18.5 vs. 65.4 ± 19.8 nmol/L, p=0.027). No association between Plant Based tertiles and protein intake was observed, however those in the third Meat Based (99.7 ± 25.1 vs. 50.9 ± 13.8 g/day, p=0.000) and Junk Food (87.4 ± 30.7 vs. 56.6 ± 22.2 g/day, p=0.000) tertile had higher protein intake compared to those in the first tertile. CONCLUSION In a healthy middle aged population with normal BMD, an increase in plant food consumption, either alone or in combination with a diet containing meat, is associated with improved bone mineralisation markers. This positive relationship is most likely due to the extensive range of micronutrients and phytochemicals packaged within plants.
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Affiliation(s)
- J Berg
- Ross Grant, The University of Sydney Adventist Hospital Clinical School, 185 Fox Valley Rd, Wahroonga, NSW Australia, Phone: +61 2 9487 9602,
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Berg J, Jablonowski R, Nordlund D, Kopic S, Bidhult S, Xanthis CG, Saeed M, Solem K, Arheden H, Carlsson M. Decreased atrioventricular plane displacement after acute myocardial infarction yields a concomitant decrease in stroke volume. J Appl Physiol (1985) 2019; 128:252-263. [PMID: 31854250 PMCID: PMC7052588 DOI: 10.1152/japplphysiol.00480.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Acute myocardial infarction (AMI) can progress to heart failure, which has a poor prognosis. Normally, 60% of stroke volume (SV) is attributed to the longitudinal ventricular shortening and lengthening evident in the atrioventricular plane displacement (AVPD) during the cardiac cycle, but there is no information on how the relationship changes between SV and AVPD before and after AMI. Therefore, the aim of this study was to determine how SV depends on AVPD before and after AMI in two swine models. Serial cardiac magnetic resonance imaging was carried out before and 1–2 h after AMI in a microembolization model (n = 12) and an ischemia-reperfusion model (n = 14). A subset of pigs (n = 7) were additionally imaged at 24 h and at 7 days. Cine and late gadolinium enhancement images were analyzed for cardiac function, AVPD measurements and infarct size estimation, respectively. AVPD decreased (P < 0.05) in all myocardial regions after AMI, with a concomitant SV decrease (P < 0.001). The ischemia-reperfusion model affected SV to a higher degree and had a larger AVPD decrease than the microembolization model (−29 ± 14% vs. −15 ± 18%; P < 0.05). Wall thickening decreased in infarcted areas (P < 0.001), and A-wave AVPD remained unchanged (P = 0.93) whereas E-wave AVPD decreased (P < 0.001) after AMI. We conclude that AVPD is coupled to SV independent of infarct type but likely to a greater degree in ischemia-reperfusion infarcts compared with microembolization infarcts. AMI reduces diastolic early filling AVPD but not AVPD from atrial contraction. These findings shed light on the physiological significance of atrioventricular plane motion when assessing acute and subacute myocardial infarction. NEW & NOTEWORTHY The link between cardiac longitudinal motion, measured as atrioventricular plane displacement (AVPD), and stroke volume (SV) is investigated in swine after acute myocardial infarction (AMI). This cardiac magnetic resonance study demonstrates a close coupling between AVPD and SV before and after AMI in an experimental setting and demonstrates that this connection is present in ischemia-reperfusion and microembolization infarcts, acutely and during the first week. Furthermore, AVPD is equally and persistently depressed in infarcted and remote myocardium after AMI.
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Affiliation(s)
- J Berg
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Clinical Physiology, Lund, Sweden
| | - R Jablonowski
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Clinical Physiology, Lund, Sweden
| | - D Nordlund
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Clinical Physiology, Lund, Sweden
| | - S Kopic
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Clinical Physiology, Lund, Sweden
| | - S Bidhult
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Clinical Physiology, Lund, Sweden
| | - C G Xanthis
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Clinical Physiology, Lund, Sweden
| | - M Saeed
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California
| | | | - H Arheden
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Clinical Physiology, Lund, Sweden
| | - M Carlsson
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Clinical Physiology, Lund, Sweden.,Department of Radiology and Biomedical Imaging, University of California, San Francisco, California
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Berg J, Lindberg M, Bengtson M, Brustugun O, Helland Å. EP1.18-12 The Neutrophil and Platelet to Lymphocyte Ratios and Glasgow Prognostic Score as a Predictor for Relapse After Stereotactic Radiation for Lung Cancer. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.2457] [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: 10/25/2022]
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Iskandar Z, Huang JTJ, Mordi I, Miller LD, Chin C, Goudie D, McWilliam C, Berg J, Neagoie A, Lang CC, Choy AM. P6505Urinary desmosine, an elastin-specific degradation product is associated with maximum aortic root size and aortic z-scores in patients with bicuspid aortic valve. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz746.1095] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Bicuspid aortic valve (BAV) is the commonest congenital cardiac abnormality affecting up to 2% of the general population. BAV is highly diverse in phenotype however a common feature is its inherent risk of morbidity and mortality from aortic root dilatation and dissection. Aortic dilatation involves elastin degradation and desmosine is an amino acid cross-link that is released into the bloodstream and urine following elastin degradation. It is known from an earlier pilot study (DESMA) of desmosine in Marfan Syndrome (MFS) patients that plasma desmosine among patients with MFS is significantly elevated and correlates with aortic size however whether this same observation is seen in other forms of inherited aortopathies such as BAV is unclear.
Objectives
1. To investigate whether patients with BAV have higher elastin degradation as indicated by plasma desmosine and urinary desmosine levels.
2. To explore the relationship between plasma and urinary desmosine levels with aortic root size in patients with BAV.
Methods
We measured urinary (ng/mg creatinine) and plasma desmosine (ng/mL) in 20 patients with BAV and healthy control subjects using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Aortic root size and corresponding Z-scores were measured on echocardiogram. Correlation was analysed with Spearman's rank test.
Results
The patients with BAV were predominantly male (n=15, 75%) with a mean age of 50.5 years ± 17.6 [SD]. All the BAV patients had normal LV systolic function and none had prior aortic root surgery or were current smokers. Nine BAV patients had treated hypertension. Compared to controls, both plasma desmosine (0.30±0.10 vs 0.26±0.075 ng/mL, p=0.01) and urinary desmosine (15.9±4.6 vs 7.2±2.8 ng/mg creatinine, p<0.001) were significantly elevated in patients with BAV. Urinary and plasma desmosine (Figure 1) were also significantly correlated (r=0.55, p=0.01). There was a significant association between urinary desmosine and maximal aortic root size and Z-scores in the BAV cohort (Figure 2) compared to controls (p=0.02), however this was not seen with plasma desmosine.
Conclusions
Urinary and plasma desmosine levels are significantly higher in patients with BAV compared to controls. Urinary desmosine is also significantly associated with maximal aortic root size, reflecting higher elastin degradation. This suggests a potential use of desmosine as a biomarker to monitor disease progression in patients with BAV.
Acknowledgement/Funding
Anonymous Trust
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Affiliation(s)
- Z Iskandar
- University of Dundee, Dundee, United Kingdom
| | - J T J Huang
- University of Dundee, Dundee, United Kingdom
| | - I Mordi
- University of Dundee, Dundee, United Kingdom
| | - L D Miller
- University of Dundee, Dundee, United Kingdom
| | - C Chin
- National Heart Centre Singapore, Singapore, Singapore
| | - D Goudie
- Ninewells Hospital, Dundee, United Kingdom
| | | | - J Berg
- Ninewells Hospital, Dundee, United Kingdom
| | - A Neagoie
- University of Dundee, Dundee, United Kingdom
| | - C C Lang
- University of Dundee, Dundee, United Kingdom
| | - A M Choy
- University of Dundee, Dundee, United Kingdom
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32
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Gouwens NW, Sorensen SA, Berg J, Lee C, Jarsky T, Ting J, Sunkin SM, Feng D, Anastassiou CA, Barkan E, Bickley K, Blesie N, Braun T, Brouner K, Budzillo A, Caldejon S, Casper T, Castelli D, Chong P, Crichton K, Cuhaciyan C, Daigle TL, Dalley R, Dee N, Desta T, Ding SL, Dingman S, Doperalski A, Dotson N, Egdorf T, Fisher M, de Frates RA, Garren E, Garwood M, Gary A, Gaudreault N, Godfrey K, Gorham M, Gu H, Habel C, Hadley K, Harrington J, Harris JA, Henry A, Hill D, Josephsen S, Kebede S, Kim L, Kroll M, Lee B, Lemon T, Link KE, Liu X, Long B, Mann R, McGraw M, Mihalas S, Mukora A, Murphy GJ, Ng L, Ngo K, Nguyen TN, Nicovich PR, Oldre A, Park D, Parry S, Perkins J, Potekhina L, Reid D, Robertson M, Sandman D, Schroedter M, Slaughterbeck C, Soler-Llavina G, Sulc J, Szafer A, Tasic B, Taskin N, Teeter C, Thatra N, Tung H, Wakeman W, Williams G, Young R, Zhou Z, Farrell C, Peng H, Hawrylycz MJ, Lein E, Ng L, Arkhipov A, Bernard A, Phillips JW, Zeng H, Koch C. Classification of electrophysiological and morphological neuron types in the mouse visual cortex. Nat Neurosci 2019; 22:1182-1195. [PMID: 31209381 PMCID: PMC8078853 DOI: 10.1038/s41593-019-0417-0] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 04/25/2019] [Indexed: 12/21/2022]
Abstract
Understanding the diversity of cell types in the brain has been an enduring challenge and requires detailed characterization of individual neurons in multiple dimensions. To systematically profile morpho-electric properties of mammalian neurons, we established a single-cell characterization pipeline using standardized patch-clamp recordings in brain slices and biocytin-based neuronal reconstructions. We built a publicly accessible online database, the Allen Cell Types Database, to display these datasets. Intrinsic physiological properties were measured from 1,938 neurons from the adult laboratory mouse visual cortex, morphological properties were measured from 461 reconstructed neurons, and 452 neurons had both measurements available. Quantitative features were used to classify neurons into distinct types using unsupervised methods. We established a taxonomy of morphologically and electrophysiologically defined cell types for this region of the cortex, with 17 electrophysiological types, 38 morphological types and 46 morpho-electric types. There was good correspondence with previously defined transcriptomic cell types and subclasses using the same transgenic mouse lines.
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Affiliation(s)
| | | | - Jim Berg
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jonathan Ting
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kris Bickley
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Nicole Blesie
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Thomas Braun
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Agata Budzillo
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Dan Castelli
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Peter Chong
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | - Tanya L Daigle
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Samuel Dingman
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Michael Fisher
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Emma Garren
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Keith Godfrey
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Melissa Gorham
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Hong Gu
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Caroline Habel
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Julie A Harris
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Alex Henry
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Sam Josephsen
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Matthew Kroll
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Brian Lee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Xiaoxiao Liu
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Medea McGraw
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Stefan Mihalas
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Sheana Parry
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jed Perkins
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - David Reid
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - David Sandman
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Corinne Teeter
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Grace Williams
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Rob Young
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Zhi Zhou
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Colin Farrell
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Hanchuan Peng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Anton Arkhipov
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington, USA.
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, Washington, USA
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Arkhipov A, Gouwens NW, Billeh YN, Gratiy S, Iyer R, Wei Z, Xu Z, Abbasi-Asl R, Berg J, Buice M, Cain N, da Costa N, de Vries S, Denman D, Durand S, Feng D, Jarsky T, Lecoq J, Lee B, Li L, Mihalas S, Ocker GK, Olsen SR, Reid RC, Soler-Llavina G, Sorensen SA, Wang Q, Waters J, Scanziani M, Koch C. Visual physiology of the layer 4 cortical circuit in silico. PLoS Comput Biol 2018; 14:e1006535. [PMID: 30419013 PMCID: PMC6258373 DOI: 10.1371/journal.pcbi.1006535] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [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: 03/23/2018] [Revised: 11/26/2018] [Accepted: 09/29/2018] [Indexed: 01/15/2023] Open
Abstract
Despite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex, quantitative modeling of cortical circuits under in-vivo-like conditions remains challenging. Here we report and publicly release a biophysically detailed circuit model of layer 4 in the mouse primary visual cortex, receiving thalamo-cortical visual inputs. The 45,000-neuron model was subjected to a battery of visual stimuli, and results were compared to published work and new in vivo experiments. Simulations reproduced a variety of observations, including effects of optogenetic perturbations. Critical to the agreement between responses in silico and in vivo were the rules of functional synaptic connectivity between neurons. Interestingly, after extreme simplification the model still performed satisfactorily on many measurements, although quantitative agreement with experiments suffered. These results emphasize the importance of functional rules of cortical wiring and enable a next generation of data-driven models of in vivo neural activity and computations. How can we capture the incredible complexity of brain circuits in quantitative models, and what can such models teach us about mechanisms underlying brain activity? To answer these questions, we set out to build extensive, bio-realistic models of brain circuitry by employing systematic datasets on brain structure and function. Here we report the first modeling results of this project, focusing on the layer 4 of the primary visual cortex (V1) of the mouse. Our simulations reproduced a variety of experimental observations in response to a large battery of visual stimuli. The results elucidated circuit mechanisms determining patters of neuronal activity in layer 4 –in particular, the roles of feedforward thalamic inputs and specific patterns of intracortical connectivity in producing tuning of neuronal responses to the orientation of motion. Simplification of neuronal models led to specific deficiencies in reproducing experimental data, giving insights into how biological details contribute to various aspects of brain activity. To enable future development of more sophisticated models, we make the software code, the model, and simulation results publicly available.
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Affiliation(s)
- Anton Arkhipov
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Nathan W Gouwens
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Yazan N Billeh
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Sergey Gratiy
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Ramakrishnan Iyer
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Ziqiang Wei
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Zihao Xu
- University of California San Diego, La Jolla, CA, United States of America
| | - Reza Abbasi-Asl
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Michael Buice
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Nicholas Cain
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Nuno da Costa
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Saskia de Vries
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Daniel Denman
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Severine Durand
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - David Feng
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Jérôme Lecoq
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Brian Lee
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Lu Li
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Stefan Mihalas
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Gabriel K Ocker
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Shawn R Olsen
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - R Clay Reid
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | | | - Staci A Sorensen
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Massimo Scanziani
- Howard Hughes Medical Institute and Department of Physiology, University of California San Francisco, San Francisco, California, United States of America
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, Washington, United States of America
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Teeter C, Iyer R, Menon V, Gouwens N, Feng D, Berg J, Szafer A, Cain N, Zeng H, Hawrylycz M, Koch C, Mihalas S. Generalized leaky integrate-and-fire models classify multiple neuron types. Nat Commun 2018; 9:709. [PMID: 29459723 PMCID: PMC5818568 DOI: 10.1038/s41467-017-02717-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 12/20/2017] [Indexed: 11/18/2022] Open
Abstract
There is a high diversity of neuronal types in the mammalian neocortex. To facilitate construction of system models with multiple cell types, we generate a database of point models associated with the Allen Cell Types Database. We construct a set of generalized leaky integrate-and-fire (GLIF) models of increasing complexity to reproduce the spiking behaviors of 645 recorded neurons from 16 transgenic lines. The more complex models have an increased capacity to predict spiking behavior of hold-out stimuli. We use unsupervised methods to classify cell types, and find that high level GLIF model parameters are able to differentiate transgenic lines comparable to electrophysiological features. The more complex model parameters also have an increased ability to differentiate between transgenic lines. Thus, creating simple models is an effective dimensionality reduction technique that enables the differentiation of cell types from electrophysiological responses without the need for a priori-defined features. This database will provide a set of simplified models of multiple cell types for the community to use in network models.
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Affiliation(s)
- Corinne Teeter
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA.
| | - Ramakrishnan Iyer
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Vilas Menon
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Dr, Ashburn, VA, 20147, USA
| | - Nathan Gouwens
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - David Feng
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Jim Berg
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Nicholas Cain
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Michael Hawrylycz
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Christof Koch
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Stefan Mihalas
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA.
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Gouwens NW, Berg J, Feng D, Sorensen SA, Zeng H, Hawrylycz MJ, Koch C, Arkhipov A. Systematic generation of biophysically detailed models for diverse cortical neuron types. Nat Commun 2018; 9:710. [PMID: 29459718 PMCID: PMC5818534 DOI: 10.1038/s41467-017-02718-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 12/20/2017] [Indexed: 01/17/2023] Open
Abstract
The cellular components of mammalian neocortical circuits are diverse, and capturing this diversity in computational models is challenging. Here we report an approach for generating biophysically detailed models of 170 individual neurons in the Allen Cell Types Database to link the systematic experimental characterization of cell types to the construction of cortical models. We build models from 3D morphologies and somatic electrophysiological responses measured in the same cells. Densities of active somatic conductances and additional parameters are optimized with a genetic algorithm to match electrophysiological features. We evaluate the models by applying additional stimuli and comparing model responses to experimental data. Applying this technique across a diverse set of neurons from adult mouse primary visual cortex, we verify that models preserve the distinctiveness of intrinsic properties between subsets of cells observed in experiments. The optimized models are accessible online alongside the experimental data. Code for optimization and simulation is also openly distributed.
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Affiliation(s)
- Nathan W Gouwens
- Allen Institute for Brain Science, 615 Westlake Avenue N, Seattle, WA, 98109, USA
| | - Jim Berg
- Allen Institute for Brain Science, 615 Westlake Avenue N, Seattle, WA, 98109, USA
| | - David Feng
- Allen Institute for Brain Science, 615 Westlake Avenue N, Seattle, WA, 98109, USA
| | - Staci A Sorensen
- Allen Institute for Brain Science, 615 Westlake Avenue N, Seattle, WA, 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, 615 Westlake Avenue N, Seattle, WA, 98109, USA
| | - Michael J Hawrylycz
- Allen Institute for Brain Science, 615 Westlake Avenue N, Seattle, WA, 98109, USA
| | - Christof Koch
- Allen Institute for Brain Science, 615 Westlake Avenue N, Seattle, WA, 98109, USA
| | - Anton Arkhipov
- Allen Institute for Brain Science, 615 Westlake Avenue N, Seattle, WA, 98109, USA.
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Riedel O, Ohlmeier C, Enders D, Elsässer A, Vizcaya D, Michel A, Eberhard S, Schlothauer N, Berg J, Garbe E. The contribution of comorbidities to mortality in hospitalized patients with heart failure. Clin Res Cardiol 2018; 107:487-497. [PMID: 29404680 DOI: 10.1007/s00392-018-1210-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/01/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND Heart failure (HF) with reduced ejection fraction (HFrEF) has a worse prognosis than HF with preserved EF (HFpEF). The study aimed to evaluate whether different comorbidity profiles of HFrEF- and HFpEF-patients or HF-specific mechanisms contribute to a greater extent to this difference. METHODS We linked data from two health insurances to data from a cardiology clinic hospital information system. Patients with a hospitalization with HF in 2005-2011, categorized as HFrEF (EF < 45%) or HFpEF (EF ≥ 45%), were propensity score (PS) matched to controls without HF on comorbidites and medication to assure similar comorbidity profiles of patients and their respective controls. The balance of the covariates in patients and controls was compared via the standardized difference (SDiff). Age-standardized 1-year mortality rates (MR) with 95% confidence intervals (CI) were calculated. RESULTS 777 HFrEF-patients (1135 HFpEF-patients) were PS-matched to 3446 (4832) controls. Balance between patients and controls was largely achieved with a SDiff < 0.1 on most variables considered. The age-standardized 1-year MRs per 1000 persons in HFrEF-patients and controls were 267.8 (95% CI 175.9-359.8) and 86.1 (95% CI 70.0-102.3). MRs in HFpEF-patients and controls were 166.2 (95% CI 101.5-230.9) and 61.5 (95% CI 52.9-70.1). Thus, differences in MRs between patients and their controls were higher for HFrEF (181.7) than for HFpEF (104.7). CONCLUSIONS Given the similar comorbidity profiles between HF-patients and controls, the higher difference in mortality rates between HFrEF-patients and controls points more to HF-specific mechanisms for these patients, whereas for HFpEF-patients a higher contribution of comorbidity is suggested by our results.
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Affiliation(s)
- Oliver Riedel
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Achterstrasse 30, 28359, Bremen, Germany.
| | - C Ohlmeier
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Achterstrasse 30, 28359, Bremen, Germany
- IGES Institut GmbH, Berlin, Germany
| | - D Enders
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Achterstrasse 30, 28359, Bremen, Germany
| | - A Elsässer
- Department of Cardiology, Klinikum Oldenburg, AöR, Oldenburg, Germany
| | - D Vizcaya
- Epidemiology, Bayer AG, Berlin, Germany
| | - A Michel
- Epidemiology, Bayer AG, Berlin, Germany
| | | | - N Schlothauer
- Hausarztpraxis Dr. Stephan Spiekermann&Partner im Gesundheitszentrum, Delmenhorst, Germany
| | - J Berg
- AOK Bremen/Bremerhaven, Bremerhaven, Germany
| | - E Garbe
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Achterstrasse 30, 28359, Bremen, Germany
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Lacassagne K, Hearon K, Berg J, Séguin B, Hoyt L, Byer B, Selmic LE. Canine spinal meningiomas and nerve sheath tumours in 34 dogs (2008-2016): Distribution and long-term outcome based upon histopathology and treatment modality. Vet Comp Oncol 2018; 16:344-351. [DOI: 10.1111/vco.12385] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 12/31/2022]
Affiliation(s)
- K. Lacassagne
- Department of Surgery; Veterinary Specialty Center of Seattle; Lynnwood Washington
| | - K. Hearon
- Department of Surgery; Metropolitan Veterinary Associates; Valley Forge Pennsylvania
| | - J. Berg
- Department of Neurology; Guardian Veterinary Specialists; Brewster New York
| | - B. Séguin
- Flint Animal Cancer Center; Colorado State University; Fort Collins Colorado
| | - L. Hoyt
- Department of Radiology; Blue Pearl; New York New York
| | - B. Byer
- College of Veterinary medicine and Biomedical Sciences; Colorado State University; Fort Collins Colorado
| | - L. E. Selmic
- Department of Veterinary Clinical Medicine, College of Veterinary medicine; University of Illinois Urbana-Champaign; Urbana Illinois
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Berg J, Halvorsen A, Bengtson M, Taskén K, Mælandsmo G, Yndestad A, Halvorsen B, Brustugun O, Aukrust P, Ueland T, Helland Å. P2.02-053 The Prognostic Value of 18 Circulating Markers of Inflammation, Endothelial Activation and Extracellular Matrix Remodeling in Non-small Cell Lung Cancer Patients. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1231] [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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39
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Marcus S, Piacquadio D, Houlihan A, Ferdon M, Berg J. LB941 Photodynamic therapy (PDT) with aminolevulinic acid (ALA) 20% and blue light reduces occurrence of actinic keratoses (AK) and de novo non-melanoma skin cancers (NMSCs) in patients with field cancerization. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.014] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Kirkland CJ, Berg J, Cummings J, Banks S. A-17Sex Differences in Hippocampal Subfield Volume: The Impact of Amyloid Burden. Arch Clin Neuropsychol 2017. [DOI: 10.1093/arclin/acx076.17] [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: 11/13/2022] Open
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Dudink EAMP, Erkuner Ö, Berg J, Nieuwlaat R, Capucci A, Camm AJ, Breithardt G, Le Heuzey JY, Luermans JGLM, Crijns HJGM. P283The influence of progression of atrial fibrillation on quality of life: a report from the euro heart survey. Europace 2017. [DOI: 10.1093/ehjci/eux141.011] [Citation(s) in RCA: 1] [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: 11/14/2022] Open
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43
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West J, Ogston S, Berg J, Palmer C, Fleming C, Kumar V, Foerster J. HLA-Cw6-positive patients with psoriasis show improved response to methotrexate treatment. Clin Exp Dermatol 2017; 42:651-655. [DOI: 10.1111/ced.13100] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2016] [Indexed: 01/22/2023]
Affiliation(s)
- J. West
- University of Dundee; College of Medicine, Dentistry, and Nursing; Dundee UK
| | - S. Ogston
- University of Dundee; College of Medicine, Dentistry, and Nursing; Dundee UK
| | - J. Berg
- University of Dundee; College of Medicine, Dentistry, and Nursing; Dundee UK
| | - C. Palmer
- University of Dundee; College of Medicine, Dentistry, and Nursing; Dundee UK
| | - C. Fleming
- Department of Dermatology and Photobiology; Ninewells Hospital; Dundee UK
| | - V. Kumar
- Department of Rheumatology; Ninewells Hospital; Dundee UK
| | - J. Foerster
- University of Dundee; College of Medicine, Dentistry, and Nursing; Dundee UK
- Department of Dermatology and Photobiology; Ninewells Hospital; Dundee UK
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44
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Pariser D, Bukhalo M, Guenthner S, Kempers S, Shideler S, Gold LS, Tschen E, Berg J, Ferdon MB, Dromgoole S. Two Multicenter, Randomized, Double-Blind, Parallel Group Comparison Studies of a Novel Enhanced Lotion Formulation of Halobetasol Propionate, 0.05% Versus Its Vehicle in Adult Subjects With Plaque Psoriasis. J Drugs Dermatol 2017; 16:234-240. [PMID: 28301619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
UNLABELLED <p>BACKGROUND: A novel lotion formulation of halobetasol propionate, 0.05% (HBP Lotion) with enhanced vehicle characteristics of a cream while preserving the ease of use and cosmetic elegance of a lotion has been developed to treat plaque psoriasis. OBJECTIVE Determine the safety and effectiveness of HBP Lotion in patients with plaque psoriasis. METHODS Two prospective, randomized, vehicle-controlled clinical studies were conducted in 443 adult subjects with moderate-severe plaque psoriasis. Subjects applied the test article to psoriatic plaques within the treatment area twice daily for 14 days. Efficacy data are based upon treatment "success" defined as those subjects that achieved scores of 0=clear or 1=almost clear with at least a two-grade improvement relative to baseline for an Investigator's Global Assessment (IGA) and clinical signs (plaque elevation, erythema, scaling). Safety data are presented as adverse events and local skin reactions. RESULTS After two weeks of treatment with HBP Lotion, 44.5% of the HBP Lotion treated subjects in each study achieved (a) treatment "success" (ie, an IGA score of 0=clear or 1=almost clear and >2 grade improvement compared to baseline) and (b) a notable reduction in plaque elevation, erythema, scaling, and pruritus. In contrast, only 6.3% and 7.1% of VEH subjects in Studies 1 and 2, respectively, achieved treatment success and the reduction of disease related signs was materially lower. Statistically, at day 15 in both Phase 3 studies, treatment success with HBP Lotion was superior to VEH (P less than 0.001). From a safety perspective the outcomes were in general unremarkable with similar findings in the HBP Lotion and VEH treatment groups. CONCLUSIONS The results demonstrate the safety and effectiveness of HBP Lotion in the treatment of plaque psoriasis. Furthermore, this novel HBP lotion formulation is also distinguished by its moisturization qualities and ease of use.</p> <p><em>J Drugs Dermatol. 2017;16(3):234-240.</em></p>.
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Berger S, Wienhold SM, Gökeri C, Behrendt U, Fatykhova D, Zscheppang K, Berg J, Gisch N, Dietert K, Doehn JM, Hocke A, Witzenrath M, Nouailles-Kursar G. Spatial and temporal regulation of neutrophil-attractant CXCL5/LIX in acute streptococcal pneumonia. Pneumologie 2017. [DOI: 10.1055/s-0037-1598372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- S Berger
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - SM Wienhold
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - C Gökeri
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - U Behrendt
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - D Fatykhova
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - K Zscheppang
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - J Berg
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - N Gisch
- Leibniz Center for Medicine and Biosciences, Research Center Borstel
| | - K Dietert
- Institute of Veterinary Pathology, Freie Universität Berlin
| | - JM Doehn
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - A Hocke
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - M Witzenrath
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
| | - G Nouailles-Kursar
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin
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El-Khoueiry A, Gitlitz B, Cole S, Tsao-Wei D, Goldkorn A, Quinn D, Lenz H, Nieva J, Dorff T, Oswald M, Berg J, Menendez X, Karakozian K, Krasnoperov V, Liu R, Thomas J, Groshen S, Gill P. A first-in-human phase I study of sEphB4-HSA in patients with advanced solid tumors with expansion at the maximum tolerated dose (MTD) or recommended phase II dose (RP2D). Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32623-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Yates TM, Turner CL, Firth HV, Berg J, Pilz DT. Baraitser-Winter cerebrofrontofacial syndrome. Clin Genet 2016; 92:3-9. [PMID: 27625340 DOI: 10.1111/cge.12864] [Citation(s) in RCA: 20] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 01/31/2023]
Abstract
Baraitser-Winter cerebrofrontofacial syndrome (BWCFF) (BRWS; MIM #243310, 614583) is a rare developmental disorder affecting multiple organ systems. It is characterised by intellectual disability (mild to severe) and distinctive facial appearance (metopic ridging/trigonocephaly, bilateral ptosis, hypertelorism). The additional presence of cortical malformations (pachygyria/lissencephaly) and ocular colobomata are also suggestive of this syndrome. Other features include moderate short stature, contractures, congenital cardiac disease and genitourinary malformations. BWCFF is caused by missense mutations in the cytoplasmic beta- and gamma-actin genes ACTB and ACTG1. We provide an overview of the clinical characteristics (including some novel findings in four recently diagnosed patients), diagnosis, management, mutation spectrum and genetic counselling.
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Affiliation(s)
- T M Yates
- Department of Medical Genetics, University of Glasgow, Glasgow, UK
| | - C L Turner
- Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, UK
| | - H V Firth
- Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - J Berg
- Department of Clinical Genetics, Ninewells Hospital, Dundee, UK
| | - D T Pilz
- West of Scotland Genetics Service, Queen Elizabeth University Hospital, Glasgow, UK
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Fleming P, Churchfield M, Scholbrock A, Clifton A, Schreck S, Johnson K, Wright A, Gebraad P, Annoni J, Naughton B, Berg J, Herges T, White J, Mikkelsen T, Sjöholm M, Angelou N. Detailed field test of yaw-based wake steering. ACTA ACUST UNITED AC 2016. [DOI: 10.1088/1742-6596/753/5/052003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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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49
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Heidemann CH, Lous J, Berg J, Christensen JJ, Håkonsen SJ, Jakobsen M, Johansen CJ, Nielsen LH, Hansen MP, Poulsen A, Schousboe LP, Skrubbeltrang C, Vind AB, Homøe P. Danish guidelines on management of otitis media in preschool children. Int J Pediatr Otorhinolaryngol 2016; 87:154-63. [PMID: 27368465 DOI: 10.1016/j.ijporl.2016.06.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Otitis media is one of the most common diseases in small children. This underlines the importance of optimizing diagnostics and treatment of the condition. Recent literature points toward a stricter approach to diagnosing acute otitis media (AOM). Moreover, ventilating tube treatment for recurrent AOM (RAOM) and chronic otitis media with effusion (COME) has become the most frequently performed surgical procedure in pre-school children. Therefore, the Danish Health and Medicines Authority and the Danish Society of Otorhinolaryngology, Head and Neck Surgery deemed it necessary to update the Danish guidelines regarding the diagnostic criteria for acute otitis media and surgical treatment of RAOM and COME. METHODS The GRADE system (The Grading of Recommendations Assessment, Development and Evaluation) was used in order to comply with current standards of evidence assessment in formulation of recommendations. An extensive literature search was conducted between July and December 2014. The quality of the existing literature was assessed using AGREE II (Appraisal of Guidelines for Research & Evaluation), AMSTAR (assessing the Methodological Quality of Systematic Reviews), QUADAS-2 (Quality of Diagnostic Accuracy Studies), Cochrane Risk of Bias Tool for randomized trials and ACROBAT-NRSI (A Cochrane Risk of Bias Assessment Tool for Non-Randomized Studies). The working group consisted of otolaryngologists, general practitioners, pediatricians, microbiologists and epidemiologists. CONCLUSION Recommendations for AOM diagnosis, surgical management for RAOM and COME, including the role of adenoidectomy and treatment of ventilating tube otorrhea, are proposed in the guideline.
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Affiliation(s)
- C H Heidemann
- Danish Health and Medicines Authority, Denmark; Department of ENT - Head & Neck Surgery, Odense University Hospital, Denmark; Department of Otorhinolaryngology, Vejle Hospital, Denmark.
| | - J Lous
- Research Unit for General Practice, Institute of Public Health, University of Southern Denmark, Denmark
| | - J Berg
- ENT Private Clinic, Århus, Denmark
| | - J J Christensen
- Department of Clinical Microbiology, Slagelse Hospital, Denmark
| | - S J Håkonsen
- Danish Health and Medicines Authority, Denmark; Centre for Clinical Guidelines, Department of Health Science and Technology, University of Aalborg, Denmark
| | - M Jakobsen
- Danish Health and Medicines Authority, Denmark
| | | | - L H Nielsen
- Department of Otorhinolaryngology, Head and Neck Surgery & Audiology, Rigshospitalet, Denmark
| | - M P Hansen
- Research Unit for General Practice, Institute of Public Health, University of Southern Denmark, Denmark; Centre for Research in Evidence-Based Practice, Bond University, Australia
| | - A Poulsen
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Denmark
| | - L P Schousboe
- Department of Otorhinolaryngology, Vejle Hospital, Denmark
| | - C Skrubbeltrang
- Danish Health and Medicines Authority, Denmark; Medical Library, Aalborg University Hospital, Denmark
| | - A B Vind
- Danish Health and Medicines Authority, Denmark
| | - P Homøe
- Department of Otorhinolaryngology and Maxillofacial Surgery, Køge University Hospital, Denmark
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50
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Blackley S, Anderson K, Berg J. A case of denosumab-induced hypocalcaemia in a patient with non-metastatic prostate cancer and renal impairment. J R Coll Physicians Edinb 2016; 45:133-5. [PMID: 26181529 DOI: 10.4997/jrcpe.2015.209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Denosumab is an emerging new treatment for osteoporosis in postmenopausal women and men with non-metastatic prostate cancer. It is largely used by specialists as an alternative treatment in patients with contraindications to traditional, more commonly used drugs such as bisphosphonates. One important side effect is hypocalcaemia, which may be life threatening. The risk of this is increased in renal impairment, mainly if eGFR < 30 ml/min/1.73m(2), and is exacerbated by vitamin D insufficiency. This is a case study of prolonged symptomatic hypocalcaemia after a single dose of denosumab in a patient with non-metastatic prostate cancer and moderate renal impairment (eGFR 40 ml/min/1.73m(2)). The patient presented with acute confusion, muscle cramps and myoclonic jerks 5 weeks after treatment. This case demonstrates the need to be aware of adverse effects of denosumab in mild-moderate renal impairment and the need to monitor calcium levels pre- and post-treatment.
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Affiliation(s)
- S Blackley
- S Blackley, Medicine of the Elderly Department, Royal Victoria Building, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK. Email
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