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  1. Article ; Online: Lawrence Baruch Cohen (1939-2023).

    Kleinfeld, David

    Neuron

    2023  Volume 111, Issue 14, Page(s) 2123–2125

    Language English
    Publishing date 2023-07-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 808167-0
    ISSN 1097-4199 ; 0896-6273
    ISSN (online) 1097-4199
    ISSN 0896-6273
    DOI 10.1016/j.neuron.2023.06.026
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    Zs.A 2496: Show issues Location:
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  2. Article ; Online: A change in behavioral state switches the pattern of motor output that underlies rhythmic head and orofacial movements.

    Liao, Song-Mao / Kleinfeld, David

    Current biology : CB

    2023  Volume 33, Issue 10, Page(s) 1951–1966.e6

    Abstract: The breathing rhythm serves as a reference that paces orofacial motor actions and orchestrates active sensing. Past work has reported that pacing occurs solely at a fixed phase relative to sniffing. We re-evaluated this constraint as a function of ... ...

    Abstract The breathing rhythm serves as a reference that paces orofacial motor actions and orchestrates active sensing. Past work has reported that pacing occurs solely at a fixed phase relative to sniffing. We re-evaluated this constraint as a function of exploratory behavior. Allocentric and egocentric rotations of the head and the electromyogenic activity of the motoneurons for head and orofacial movements were recorded in free-ranging rats as they searched for food. We found that a change in state from foraging to rearing is accompanied by a large phase shift in muscular activation relative to sniffing, and a concurrent change in the frequency of sniffing, so that pacing now occurs at one of the two phases. Further, head turning is biased such that an animal gathers a novel sample of its environment upon inhalation. In total, the coordination of active sensing has a previously unrealized computational complexity. This can emerge from hindbrain circuits with fixed architecture and credible synaptic time delays.
    MeSH term(s) Rats ; Animals ; Vibrissae/physiology ; Movement/physiology ; Exploratory Behavior/physiology ; Rhombencephalon ; Motor Neurons ; Head Movements/physiology
    Language English
    Publishing date 2023-04-26
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2023.04.008
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  3. Article ; Online: Elephant trunks: Strength and dexterity from mini-fascicles.

    Olson, William / Zhang, Linghua / O'Connor, Daniel H / Kleinfeld, David

    Current biology : CB

    2024  Volume 33, Issue 22, Page(s) R1203–R1205

    Abstract: Muscular hydrostats, such as the elephant trunk, can perform precise motor actions. A new study has revealed that the elephant trunk contains a dense network of tiny muscle fascicles, suggesting that muscle miniaturization may be a key toward ... ...

    Abstract Muscular hydrostats, such as the elephant trunk, can perform precise motor actions. A new study has revealed that the elephant trunk contains a dense network of tiny muscle fascicles, suggesting that muscle miniaturization may be a key toward understanding how soft organs achieve both strength and dexterity.
    MeSH term(s) Animals ; Elephants ; Muscle, Skeletal
    Language English
    Publishing date 2024-04-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2023.10.012
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  4. Article ; Online: PIP

    Earley, Scott / Kleinfeld, David

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 21

    MeSH term(s) Cerebrovascular Circulation ; Neurovascular Coupling ; Phosphatidylinositol 4,5-Diphosphate
    Chemical Substances Phosphatidylinositol 4,5-Diphosphate
    Language English
    Publishing date 2021-05-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2106308118
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    Zs.A 1148: Show issues Location:
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  5. Article ; Online: Roger Tsien 1952-2016.

    Kleinfeld, David

    Nature neuroscience

    2016  Volume 19, Issue 10, Page(s) 1269–1270

    Language English
    Publishing date 2016-09-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1420596-8
    ISSN 1546-1726 ; 1097-6256
    ISSN (online) 1546-1726
    ISSN 1097-6256
    DOI 10.1038/nn.4410
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  6. Article: CellBoost: A pipeline for machine assisted annotation in Neuroanatomy.

    Qian, Kui / Friedman, Beth / Takatoh, Jun / Wang, Fan / Kleinfeld, David / Freund, Yoav

    bioRxiv : the preprint server for biology

    2024  

    Abstract: One of the important yet labor intensive tasks in neuroanatomy is the identification of select populations of cells. Current high-throughput techniques enable marking cells with histochemical fluorescent molecules as well as through the genetic ... ...

    Abstract One of the important yet labor intensive tasks in neuroanatomy is the identification of select populations of cells. Current high-throughput techniques enable marking cells with histochemical fluorescent molecules as well as through the genetic expression of fluorescent proteins. Modern scanning microscopes allow high resolution multi-channel imaging of the mechanically or optically sectioned brain with thousands of marked cells per square millimeter. Manual identification of all marked cells is prohibitively time consuming. At the same time, simple segmentation algorithms suffer from high error rates and sensitivity to variation in fluorescent intensity and spatial distribution. We present a methodology that combines human judgement and machine learning that serves to significantly reduce the labor of the anatomist while improving the consistency of the annotation. As a demonstration, we analyzed murine brains with marked premotor neurons in the brainstem. We compared the error rate of our method to the disagreement rate among human anatomists. This comparison shows that our method can reduce the time to annotate by as much as ten-fold without significantly increasing the rate of errors. We show that our method achieves significant reduction in labor while achieving an accuracy that is similar to the level of agreement between different anatomists.
    Language English
    Publishing date 2024-01-21
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.13.557658
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  7. Article: Guide to the construction and use of an adaptive optics two-photon microscope with direct wavefront sensing.

    Yao, Pantong / Liu, Rui / Broginni, Thomas / Thunemann, Martin / Kleinfeld, David

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Two-photon microscopy, combined with appropriate optical labeling, has enabled the study of structure and function throughout nervous systems. This methodology enables, for example, the measurement and tracking of sub-micrometer structures within brain ... ...

    Abstract Two-photon microscopy, combined with appropriate optical labeling, has enabled the study of structure and function throughout nervous systems. This methodology enables, for example, the measurement and tracking of sub-micrometer structures within brain cells, the spatio-temporal mapping of spikes in individual neurons, and the spatio-temporal mapping of transmitter release in individual synapses. Yet the spatial resolution of two-photon microscopy rapidly degrades as imaging is attempted at depths more than a few scattering lengths into tissue, i.e., below the superficial layers that constitute the top 300 to 400 µm of neocortex. To obviate this limitation, we measure the wavefront at the focus of the excitation beam and utilize adaptive optics that alters the incident wavefront to achieve an improved focal volume. We describe the constructions, calibration, and operation of a two-photon microscopy that incorporates adaptive optics to restore diffraction-limited resolution throughout the nearly 900 µm depth of mouse cortex. Our realization utilizes a guide star formed by excitation of red-shifted dye within the blood serum to directly measure the wavefront. We incorporate predominantly commercial optical, optomechanical, mechanical, and electronic components; computer aided design models of the exceptional custom components are supplied. The design is modular and allows for expanded imaging and optical excitation capabilities. We demonstrate our methodology in mouse neocortex by imaging the morphology of somatostatin-expressing neurons at 700 µm beneath the pia, calcium dynamics of layer 5b projection neurons, and glutamate transmission to L4 neurons.
    Language English
    Publishing date 2023-01-24
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.24.525307
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  8. Article ; Online: Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing.

    Yao, Pantong / Liu, Rui / Broggini, Thomas / Thunemann, Martin / Kleinfeld, David

    Nature protocols

    2023  Volume 18, Issue 12, Page(s) 3732–3766

    Abstract: Two-photon microscopy, combined with the appropriate optical labelling, enables the measurement and tracking of submicrometer structures within brain cells, as well as the spatiotemporal mapping of spikes in individual neurons and of neurotransmitter ... ...

    Abstract Two-photon microscopy, combined with the appropriate optical labelling, enables the measurement and tracking of submicrometer structures within brain cells, as well as the spatiotemporal mapping of spikes in individual neurons and of neurotransmitter release in individual synapses. Yet, the spatial resolution of two-photon microscopy rapidly degrades as imaging is attempted at depths of more than a few scattering lengths into tissue, i.e., below the superficial layers that constitute the top 300-400 µm of the neocortex. To obviate this limitation, we shape the focal volume, generated by the excitation beam, by modulating the incident wavefront via guidestar-assisted adaptive optics. Here, we describe the construction, calibration and operation of a two-photon microscope that incorporates adaptive optics to restore diffraction-limited resolution at depths close to 900 µm in the mouse cortex. Our setup detects a guidestar formed by the excitation of a red-shifted dye in blood serum, used to directly measure the wavefront. We incorporate predominantly commercially available optical, optomechanical, mechanical and electronic components, and supply computer-aided design models of other customized components. The resulting adaptive optics two-photon microscope is modular and allows for expanded imaging and optical excitation capabilities. We demonstrate our methodology in the mouse neocortex by imaging the morphology of somatostatin-expressing neurons that lie 700 µm beneath the pia, calcium dynamics of layer 5b projection neurons and thalamocortical glutamate transmission to L4 neurons. The protocol requires ~30 d to complete and is suitable for users with graduate-level expertise in optics.
    MeSH term(s) Mice ; Animals ; Microscopy ; Optics and Photonics ; Photons ; Neurons ; Calcium
    Chemical Substances Calcium (SY7Q814VUP)
    Language English
    Publishing date 2023-11-01
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-023-00893-w
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  9. Article ; Online: A brainstem circuit for the expression of defensive facial reactions in rat.

    Callado Pérez, Amalia / Demers, Maxime / Fassihi, Arash / Moore, Jeffrey D / Kleinfeld, David / Deschênes, Martin

    Current biology : CB

    2023  Volume 33, Issue 18, Page(s) 4030–4035.e3

    Abstract: The brainstem houses neuronal circuits that control homeostasis of vital functions. These include the depth and rate of ... ...

    Abstract The brainstem houses neuronal circuits that control homeostasis of vital functions. These include the depth and rate of breathing
    MeSH term(s) Rats ; Animals ; Apnea ; Ammonia ; Brain Stem/physiology ; Vagus Nerve ; Neurons
    Chemical Substances Ammonia (7664-41-7)
    Language English
    Publishing date 2023-09-12
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2023.08.041
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  10. Article ; Online: Interchangeable Role of Motor Cortex and Reafference for the Stable Execution of an Orofacial Action.

    Elbaz, Michaël A / Demers, Maxime / Kleinfeld, David / Ethier, Christian / Deschênes, Martin

    The Journal of neuroscience : the official journal of the Society for Neuroscience

    2023  Volume 43, Issue 30, Page(s) 5521–5536

    Abstract: Animals interact with their environment through mechanically active, mobile sensors. The efficient use of these sensory organs implies the ability to track their position; otherwise, perceptual stability or prehension would be profoundly impeded. The ... ...

    Abstract Animals interact with their environment through mechanically active, mobile sensors. The efficient use of these sensory organs implies the ability to track their position; otherwise, perceptual stability or prehension would be profoundly impeded. The nervous system may keep track of the position of a sensorimotor organ via two complementary feedback mechanisms-peripheral reafference (external, sensory feedback) and efference copy (internal feedback). Yet, the potential contributions of these mechanisms remain largely unexplored. By training male rats to place one of their vibrissae within a predetermined angular range without contact, a task that depends on knowledge of vibrissa position relative to their face, we found that peripheral reafference is not required. The presence of motor cortex is not required either, except in the absence of peripheral reafference to maintain motor stability. Finally, the red nucleus, which receives descending inputs from motor cortex and cerebellum and projects to facial motoneurons, is critically involved in the execution of the vibrissa positioning task. All told, our results point toward the existence of an internal model that requires either peripheral reafference or motor cortex to optimally drive voluntary motion.
    MeSH term(s) Rats ; Animals ; Male ; Motor Cortex ; Motor Neurons/physiology ; Nervous System Physiological Phenomena ; Cerebellum/physiology ; Vibrissae/physiology ; Somatosensory Cortex/physiology
    Language English
    Publishing date 2023-07-03
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 604637-x
    ISSN 1529-2401 ; 0270-6474
    ISSN (online) 1529-2401
    ISSN 0270-6474
    DOI 10.1523/JNEUROSCI.2089-22.2023
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