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ackman678
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OMEGA.bib
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OMEGA.bib
@@ -3813,6 +3813,41 @@ SIGNIFICANCE STATEMENT: Cortical activity is an important indicator of long-term
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url = {papers/Ackman_JNeurosci2009.pdf},
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url = {papers/Ackman_JNeurosci2009.pdf},
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Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4093-08.2009}}
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Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4093-08.2009}}
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@article{Perna2021,
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title = {Perinatal Penicillin Exposure Affects Cortical Development and Sensory Processing.},
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author = {Perna, James and Lu, Ju and Mullen, Brian and Liu, Taohui and Tjia, Michelle and Weiser, Sydney and Ackman, James and Zuo, Yi},
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journal = {Front Mol Neurosci},
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volume = {14},
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year = {2021},
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pages = {704219},
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abstract = {The prevalent use of antibiotics in pregnant women and neonates raises concerns about long-term risks for children's health, but their effects on the central nervous system is not well understood. We studied the effects of perinatal penicillin exposure (PPE) on brain structure and function in mice with a therapeutically relevant regimen. We used a battery of behavioral tests to evaluate anxiety, working memory, and sensory processing, and immunohistochemistry to quantify changes in parvalbumin-expressing inhibitory interneurons (PV+ INs), perineuronal nets (PNNs), as well as microglia density and morphology. In addition, we performed mesoscale calcium imaging to study neural activity and functional connectivity across cortical regions, and two-photon imaging to monitor dendritic spine and microglial dynamics. We found that adolescent PPE mice have abnormal sensory processing, including impaired texture discrimination and altered prepulse inhibition. Such behavioral changes are associated with increased spontaneous neural activities in various cortical regions, and delayed maturation of PV+ INs in the somatosensory cortex. Furthermore, adolescent PPE mice have elevated elimination of dendritic spines on the apical dendrites of layer 5 pyramidal neurons, as well as increased ramifications and spatial coverage of cortical microglia. Finally, while synaptic defects are transient during adolescence, behavioral abnormalities persist into adulthood. Our study demonstrates that early-life exposure to antibiotics affects cortical development, leaving a lasting effect on brain functions.},
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pmid = {35002614},
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doi = {10.3389/fnmol.2021.704219},
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pmc = {PMC8727458},
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url = {papers/Perna_FrontMolNeurosci2022-35002614.pdf},
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nlmuniqueid = {101477914}
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}
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@article{Lu2021,
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title = {An analog of psychedelics restores functional neural circuits disrupted by unpredictable stress.},
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author = {Lu, Ju and Tjia, Michelle and Mullen, Brian and Cao, Bing and Lukasiewicz, Kacper and Shah-Morales, Sajita and Weiser, Sydney and Cameron, Lindsay P and Olson, David E and Chen, Lu and Zuo, Yi},
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journal = {Mol Psychiatry},
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volume = {26},
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number = {11},
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year = {2021},
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month = {11},
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pages = {6237-6252},
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abstract = {Psychological stress affects a wide spectrum of brain functions and poses risks for many mental disorders. However, effective therapeutics to alleviate or revert its deleterious effects are lacking. A recently synthesized psychedelic analog tabernanthalog (TBG) has demonstrated anti-addictive and antidepressant potential. Whether TBG can rescue stress-induced affective, sensory, and cognitive deficits, and how it may achieve such effects by modulating neural circuits, remain unknown. Here we show that in mice exposed to unpredictable mild stress (UMS), administration of a single dose of TBG decreases their anxiety level and rescues deficits in sensory processing as well as in cognitive flexibility. Post-stress TBG treatment promotes the regrowth of excitatory neuron dendritic spines lost during UMS, decreases the baseline neuronal activity, and enhances whisking-modulation of neuronal activity in the somatosensory cortex. Moreover, calcium imaging in head-fixed mice performing a whisker-dependent texture discrimination task shows that novel textures elicit responses from a greater proportion of neurons in the somatosensory cortex than do familiar textures. Such differential response is diminished by UMS and is restored by TBG. Together, our study reveals the effects of UMS on cortical neuronal circuit activity patterns and demonstrate that TBG combats the detrimental effects of stress by modulating basal and stimulus-dependent neural activity in cortical networks.},
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keywords = {Animals; Hallucinogens; Mice; Neurons; Somatosensory Cortex; Vibrissae; },
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pmid = {34035476},
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doi = {10.1038/s41380-021-01159-1},
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pii = {10.1038/s41380-021-01159-1},
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pmc = {PMC8613316},
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mid = {NIHMS1701193},
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url = {papers/Lu_MolPsychiatry2022-34035476.pdf},
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nlmuniqueid = {9607835}
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}
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@article{Veinante:2003,
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@article{Veinante:2003,
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Abstract = {In freely moving rats, whisking is associated with a slow modulation of neuronal excitability in the primary somatosensory cortex. Because it persists after the blockade of vibrissa input, it was suggested that the slow modulation might be mediated by motor-sensory corticocortical connections and perhaps result from the corollary discharges of corticofugal cells. In the present study, we identified motor cortical cells that project to the barrel field and reconstructed their axonal projections after juxtacellularly staining single cells with a biotinylated tracer. On the basis of the final destination of main axons, two groups of neurons contribute to motor-sensory projections: callosal cells (87.5%) and corticofugal cells (12.5%). Axon collaterals of callosal cells arborize in layers five to six of the granular and dysgranular zones and give off several branches that ascend between the barrels to ramify in the molecular layer. In contrast, the axon collaterals of corticofugal cells do not ramify in the infragranular layers but in layer 1. The origin of the majority of motor sensory projections from callosally projecting cells does not support the notion that the slow modulation results from the corollary discharges of corticofugal axons. It would rather originate from a separate population of cells, which could output the slow signal to the barrel field in parallel with the corticofugal commands to a brainstem pattern generator. As free whisking is characterized by bilateral concerted movements of the vibrissae, the transcallosal contribution of motor-sensory axons represents a substrate for synchronizing the slow modulation across both hemispheres.},
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Abstract = {In freely moving rats, whisking is associated with a slow modulation of neuronal excitability in the primary somatosensory cortex. Because it persists after the blockade of vibrissa input, it was suggested that the slow modulation might be mediated by motor-sensory corticocortical connections and perhaps result from the corollary discharges of corticofugal cells. In the present study, we identified motor cortical cells that project to the barrel field and reconstructed their axonal projections after juxtacellularly staining single cells with a biotinylated tracer. On the basis of the final destination of main axons, two groups of neurons contribute to motor-sensory projections: callosal cells (87.5%) and corticofugal cells (12.5%). Axon collaterals of callosal cells arborize in layers five to six of the granular and dysgranular zones and give off several branches that ascend between the barrels to ramify in the molecular layer. In contrast, the axon collaterals of corticofugal cells do not ramify in the infragranular layers but in layer 1. The origin of the majority of motor sensory projections from callosally projecting cells does not support the notion that the slow modulation results from the corollary discharges of corticofugal axons. It would rather originate from a separate population of cells, which could output the slow signal to the barrel field in parallel with the corticofugal commands to a brainstem pattern generator. As free whisking is characterized by bilateral concerted movements of the vibrissae, the transcallosal contribution of motor-sensory axons represents a substrate for synchronizing the slow modulation across both hemispheres.},
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Author = {Veinante, Pierre and Desch{\^e}nes, Martin},
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Author = {Veinante, Pierre and Desch{\^e}nes, Martin},
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@@ -112799,7 +112834,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
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pages = {191-5},
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pages = {191-5},
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abstract = {Nerve impulses are propagated at nodes of Ranvier in the myelinated nerves of vertebrates. Internodal distances have been proposed to affect the velocity of nerve impulse conduction; however, direct evidence is lacking, and the cellular mechanisms that might regulate the length of the myelinated segments are unknown. Ramón y Cajal described longitudinal and transverse bands of cytoplasm or trabeculae in internodal Schwann cells and suggested that they had a nutritive function. Here we show that internodal growth in wild-type nerves is precisely matched to nerve extension, but disruption of the cytoplasmic bands in Periaxin-null mice impairs Schwann cell elongation during nerve growth. By contrast, myelination proceeds normally. The capacity of wild-type and mutant Schwann cells to elongate is cell-autonomous, indicating that passive stretching can account for the lengthening of the internode during limb growth. As predicted on theoretical grounds, decreased internodal distances strikingly decrease conduction velocities and so affect motor function. We propose that microtubule-based transport in the longitudinal bands of Cajal permits internodal Schwann cells to lengthen in response to axonal growth, thus ensuring rapid nerve impulse transmission.},
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abstract = {Nerve impulses are propagated at nodes of Ranvier in the myelinated nerves of vertebrates. Internodal distances have been proposed to affect the velocity of nerve impulse conduction; however, direct evidence is lacking, and the cellular mechanisms that might regulate the length of the myelinated segments are unknown. Ramón y Cajal described longitudinal and transverse bands of cytoplasm or trabeculae in internodal Schwann cells and suggested that they had a nutritive function. Here we show that internodal growth in wild-type nerves is precisely matched to nerve extension, but disruption of the cytoplasmic bands in Periaxin-null mice impairs Schwann cell elongation during nerve growth. By contrast, myelination proceeds normally. The capacity of wild-type and mutant Schwann cells to elongate is cell-autonomous, indicating that passive stretching can account for the lengthening of the internode during limb growth. As predicted on theoretical grounds, decreased internodal distances strikingly decrease conduction velocities and so affect motor function. We propose that microtubule-based transport in the longitudinal bands of Cajal permits internodal Schwann cells to lengthen in response to axonal growth, thus ensuring rapid nerve impulse transmission.},
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keywords = {Animals; Axons; Behavior, Animal; Cell Size; Cytoplasm; Gene Deletion; Membrane Proteins; Mice; Mice, Knockout; Microtubules; Muscle, Skeletal; Myelin Basic Protein; Nerve Fibers, Myelinated; RNA, Messenger; Schwann Cells; Sciatic Nerve; Synaptic Transmission; },
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keywords = {Animals; Axons; Behavior, Animal; Cell Size; Cytoplasm; Gene Deletion; Membrane Proteins; Mice; Mice, Knockout; Microtubules; Muscle, Skeletal; Myelin Basic Protein; Nerve Fibers, Myelinated; RNA, Messenger; Schwann Cells; Sciatic Nerve; Synaptic Transmission; },
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pubmed = {15356632},
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pmid = {15356632},
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doi = {10.1038/nature02841},
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doi = {10.1038/nature02841},
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pii = {nature02841},
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pii = {nature02841},
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url = {papers/Court_Nature2004-15356632.pdf},
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url = {papers/Court_Nature2004-15356632.pdf},
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@@ -112817,7 +112852,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
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pages = {210-8},
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pages = {210-8},
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abstract = {Enhanced neuronal activity in the brain triggers a local increase in blood flow, termed functional hyperemia, via several mechanisms, including calcium (Ca(2+)) signaling in astrocytes. However, recent in vivo studies have questioned the role of astrocytes in functional hyperemia because of the slow and sparse dynamics of their somatic Ca(2+) signals and the absence of glutamate metabotropic receptor 5 in adults. Here, we reexamined their role in neurovascular coupling by selectively expressing a genetically encoded Ca(2+) sensor in astrocytes of the olfactory bulb. We show that in anesthetized mice, the physiological activation of olfactory sensory neuron (OSN) terminals reliably triggers Ca(2+) increases in astrocyte processes but not in somata. These Ca(2+) increases systematically precede the onset of functional hyperemia by 1-2 s, reestablishing astrocytes as potential regulators of neurovascular coupling. },
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abstract = {Enhanced neuronal activity in the brain triggers a local increase in blood flow, termed functional hyperemia, via several mechanisms, including calcium (Ca(2+)) signaling in astrocytes. However, recent in vivo studies have questioned the role of astrocytes in functional hyperemia because of the slow and sparse dynamics of their somatic Ca(2+) signals and the absence of glutamate metabotropic receptor 5 in adults. Here, we reexamined their role in neurovascular coupling by selectively expressing a genetically encoded Ca(2+) sensor in astrocytes of the olfactory bulb. We show that in anesthetized mice, the physiological activation of olfactory sensory neuron (OSN) terminals reliably triggers Ca(2+) increases in astrocyte processes but not in somata. These Ca(2+) increases systematically precede the onset of functional hyperemia by 1-2 s, reestablishing astrocytes as potential regulators of neurovascular coupling. },
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keywords = {Animals; Astrocytes; Calcium Signaling; Cerebrovascular Circulation; Mice; Mice, Transgenic; Olfactory Bulb; Olfactory Receptor Neurons; Receptor, Metabotropic Glutamate 5; Synapses; },
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keywords = {Animals; Astrocytes; Calcium Signaling; Cerebrovascular Circulation; Mice; Mice, Transgenic; Olfactory Bulb; Olfactory Receptor Neurons; Receptor, Metabotropic Glutamate 5; Synapses; },
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pubmed = {25531572},
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pmid = {25531572},
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pii = {nn.3906},
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pii = {nn.3906},
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doi = {10.1038/nn.3906},
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doi = {10.1038/nn.3906},
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pmc = {PMC4651918},
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pmc = {PMC4651918},
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@@ -112836,7 +112871,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
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pages = {77-95},
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pages = {77-95},
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abstract = {Of all brain regions, the 6-layered neocortex has undergone the most dramatic changes in size and complexity during mammalian brain evolution. These changes, occurring in the context of a conserved set of organizational features that emerge through stereotypical developmental processes, are considered responsible for the cognitive capacities and sensory specializations represented within the mammalian clade. The modern experimental era of developmental neurobiology, spanning 6 decades, has deciphered a number of mechanisms responsible for producing the diversity of cortical neuron types, their precise connectivity and the role of gene by environment interactions. Here, experiments providing insight into the development of cortical projection neuron differentiation and connectivity are reviewed. This current perspective integrates discussion of classic studies and new findings, based on recent technical advances, to highlight an improved understanding of the neuronal complexity and precise connectivity of cortical circuitry. These descriptive advances bring new opportunities for studies related to the developmental origins of cortical circuits that will, in turn, improve the prospects of identifying pathogenic targets of neurodevelopmental disorders.},
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abstract = {Of all brain regions, the 6-layered neocortex has undergone the most dramatic changes in size and complexity during mammalian brain evolution. These changes, occurring in the context of a conserved set of organizational features that emerge through stereotypical developmental processes, are considered responsible for the cognitive capacities and sensory specializations represented within the mammalian clade. The modern experimental era of developmental neurobiology, spanning 6 decades, has deciphered a number of mechanisms responsible for producing the diversity of cortical neuron types, their precise connectivity and the role of gene by environment interactions. Here, experiments providing insight into the development of cortical projection neuron differentiation and connectivity are reviewed. This current perspective integrates discussion of classic studies and new findings, based on recent technical advances, to highlight an improved understanding of the neuronal complexity and precise connectivity of cortical circuitry. These descriptive advances bring new opportunities for studies related to the developmental origins of cortical circuits that will, in turn, improve the prospects of identifying pathogenic targets of neurodevelopmental disorders.},
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keywords = {Axon guidance; Cell type specification; Cerebral cortex; Circuits; Connectivity; Excitatory neurons; Experience; Genetics; Histogenesis; Human; Microcircuit; Neural network; Refinement; Reprogramming; Rodent; Specification; Synaptic specificity; Synaptogenesis; Thalamus; Animals; Humans; Neocortex; Nerve Net; Neural Pathways; Neural Stem Cells; Neurogenesis; Neurons; },
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keywords = {Axon guidance; Cell type specification; Cerebral cortex; Circuits; Connectivity; Excitatory neurons; Experience; Genetics; Histogenesis; Human; Microcircuit; Neural network; Refinement; Reprogramming; Rodent; Specification; Synaptic specificity; Synaptogenesis; Thalamus; Animals; Humans; Neocortex; Nerve Net; Neural Pathways; Neural Stem Cells; Neurogenesis; Neurons; },
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pubmed = {30677429},
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pmid = {30677429},
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pii = {S0301-0082(18)30136-9},
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pii = {S0301-0082(18)30136-9},
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doi = {10.1016/j.pneurobio.2019.01.003},
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doi = {10.1016/j.pneurobio.2019.01.003},
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pmc = {PMC6402587},
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pmc = {PMC6402587},
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@@ -112856,7 +112891,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
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pages = {370-92},
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pages = {370-92},
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abstract = {Pyramidal neurons within the cerebral cortex are known to make long-range horizontal connections via an extensive axonal collateral system. The synaptic characteristics and specificities of these connections were studied at the ultrastructural level. Two superficial layer pyramidal cells in the primate striate cortex were labeled by intracellular injections with horseradish peroxidase (HRP) and their axon terminals were subsequently examined with the technique of electron microscopic (EM) serial reconstruction. At the light microscopic level both cells showed the characteristic pattern of widespread, clustered axon collaterals. We examined collateral clusters located near the dendritic field (proximal) and approximately 0.5 mm away (distal). The synapses were of the asymmetric/round vesicle variety (type I), and were therefore presumably excitatory. Three-quarters of the postsynaptic targets were the dendritic spines of other pyramidal cells. A few of the axodendritic synapses were with the shafts of pyramidal cells, bringing the proportion of pyramidal cell targets to 80%. The remaining labeled endings were made with the dendritic shafts of smooth stellate cells, which are presumed to be (GABA)ergic inhibitory cells. On the basis of serial reconstruction of a few of these cells and their dendrites, a likely candidate for one target inhibitory cell is the small-medium basket cell. Taken together, this pattern of outputs suggests a mixture of postsynaptic effects mediated by consequence the horizontal connections may well be the substrate for the variety of influences observed between the receptive field center and its surround.},
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abstract = {Pyramidal neurons within the cerebral cortex are known to make long-range horizontal connections via an extensive axonal collateral system. The synaptic characteristics and specificities of these connections were studied at the ultrastructural level. Two superficial layer pyramidal cells in the primate striate cortex were labeled by intracellular injections with horseradish peroxidase (HRP) and their axon terminals were subsequently examined with the technique of electron microscopic (EM) serial reconstruction. At the light microscopic level both cells showed the characteristic pattern of widespread, clustered axon collaterals. We examined collateral clusters located near the dendritic field (proximal) and approximately 0.5 mm away (distal). The synapses were of the asymmetric/round vesicle variety (type I), and were therefore presumably excitatory. Three-quarters of the postsynaptic targets were the dendritic spines of other pyramidal cells. A few of the axodendritic synapses were with the shafts of pyramidal cells, bringing the proportion of pyramidal cell targets to 80%. The remaining labeled endings were made with the dendritic shafts of smooth stellate cells, which are presumed to be (GABA)ergic inhibitory cells. On the basis of serial reconstruction of a few of these cells and their dendrites, a likely candidate for one target inhibitory cell is the small-medium basket cell. Taken together, this pattern of outputs suggests a mixture of postsynaptic effects mediated by consequence the horizontal connections may well be the substrate for the variety of influences observed between the receptive field center and its surround.},
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keywords = {Animals; Axonal Transport; Axons; Cerebral Cortex; Dendrites; Horseradish Peroxidase; Macaca fascicularis; Microscopy, Electron; Pyramidal Tracts; Synapses; Visual Cortex; },
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keywords = {Animals; Axonal Transport; Axons; Cerebral Cortex; Dendrites; Horseradish Peroxidase; Macaca fascicularis; Microscopy, Electron; Pyramidal Tracts; Synapses; Visual Cortex; },
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pubmed = {1709953},
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pmid = {1709953},
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doi = {10.1002/cne.903050303},
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doi = {10.1002/cne.903050303},
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url = {papers/McGuire_JCompNeurol1991-1709953.pdf},
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url = {papers/McGuire_JCompNeurol1991-1709953.pdf},
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nlmuniqueid = {0406041}
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nlmuniqueid = {0406041}
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@@ -112872,7 +112907,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
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month = {Sep},
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month = {Sep},
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pages = {55-80},
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pages = {55-80},
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keywords = {Animals; Cerebral Cortex; Cybernetics; Electrophysiology; Humans; Mathematics; Models, Neurological; Rabbits; Thalamus; },
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keywords = {Animals; Cerebral Cortex; Cybernetics; Electrophysiology; Humans; Mathematics; Models, Neurological; Rabbits; Thalamus; },
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pubmed = {4767470},
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pmid = {4767470},
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doi = {10.1007/BF00288786},
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doi = {10.1007/BF00288786},
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url = {papers/Wilson_Kybernetik1973-4767470.pdf},
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url = {papers/Wilson_Kybernetik1973-4767470.pdf},
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nlmuniqueid = {7502604}
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nlmuniqueid = {7502604}
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@@ -112889,7 +112924,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
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pages = {41-58},
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pages = {41-58},
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abstract = {The intrinsic connectivity of striate cortex was investigated by injecting horseradish peroxidase (HRP) into this area in tree shrews. Such HRP injections demonstrated periodically organized, stripelike connections within area 17. These stripes occur in layers I-IIIA and consist of a small number or retrogradely filled neurons, some clearly pyramidal, together with HRP-labeled axon terminals. HRP-filled axons trunks run between labeled stripes, interconnecting adjacent and distant regions of the stripe pattern. Correlation with Golgi-stained tissue suggests that these stripes are horizontally interconnected by pyramidal neurons with long intracortical axon collaterals (followed for distances over 1 mm from the soma). The HRP-labeled strips measure about 230 micrometers in width, with a center-to-center repeat distance of 450--500 micrometers. They have been mapped over an 8 mm2 area of striate cortex and would thus seem capable of effecting lateral interactions over considerable portions of the retinotopic map. In their dimensions and overall pattern, these anatomical stripes resemble the 2-deoxyglucose (2-DG) bands resulting from visual stimulation of trees shrews with stripes of a single orientation. While the functional role of the HRP-labeled stripes is unclear, their similarities with the 2-DG pattern raise the intriguing possibility that they may be related to orientation selectivity. The striking regularity of these extensive lateral interconnections emphasizes the importance of horizontal intralaminar connections within the cortex.},
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abstract = {The intrinsic connectivity of striate cortex was investigated by injecting horseradish peroxidase (HRP) into this area in tree shrews. Such HRP injections demonstrated periodically organized, stripelike connections within area 17. These stripes occur in layers I-IIIA and consist of a small number or retrogradely filled neurons, some clearly pyramidal, together with HRP-labeled axon terminals. HRP-filled axons trunks run between labeled stripes, interconnecting adjacent and distant regions of the stripe pattern. Correlation with Golgi-stained tissue suggests that these stripes are horizontally interconnected by pyramidal neurons with long intracortical axon collaterals (followed for distances over 1 mm from the soma). The HRP-labeled strips measure about 230 micrometers in width, with a center-to-center repeat distance of 450--500 micrometers. They have been mapped over an 8 mm2 area of striate cortex and would thus seem capable of effecting lateral interactions over considerable portions of the retinotopic map. In their dimensions and overall pattern, these anatomical stripes resemble the 2-deoxyglucose (2-DG) bands resulting from visual stimulation of trees shrews with stripes of a single orientation. While the functional role of the HRP-labeled stripes is unclear, their similarities with the 2-DG pattern raise the intriguing possibility that they may be related to orientation selectivity. The striking regularity of these extensive lateral interconnections emphasizes the importance of horizontal intralaminar connections within the cortex.},
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keywords = {Animals; Autoradiography; Brain Mapping; Corpus Callosum; Deoxyglucose; Genetic Variation; Horseradish Peroxidase; Tupaia; Tupaiidae; Visual Cortex; },
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keywords = {Animals; Autoradiography; Brain Mapping; Corpus Callosum; Deoxyglucose; Genetic Variation; Horseradish Peroxidase; Tupaia; Tupaiidae; Visual Cortex; },
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pubmed = {7119173},
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pmid = {7119173},
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doi = {10.1002/cne.902090105},
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doi = {10.1002/cne.902090105},
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url = {papers/Rockland_JCompNeurol1982-7119173.pdf},
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url = {papers/Rockland_JCompNeurol1982-7119173.pdf},
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nlmuniqueid = {0406041}
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nlmuniqueid = {0406041}
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@@ -112906,7 +112941,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
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pages = {441-52},
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pages = {441-52},
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abstract = {Artificial neural networks are usually built on rather few elements such as activation functions, learning rules, and the network topology. When modelling the more complex properties of realistic networks, however, a number of higher-level structural principles become important. In this paper we present a theoretical framework for modelling cortical networks at a high level of abstraction. Based on the notion of a population of neurons, this framework can accommodate the common features of cortical architecture, such as lamination, multiple areas and topographic maps, input segregation, and local variations of the frequency of different cell types (e.g., cytochrome oxidase blobs). The framework is meant primarily for the simulation of activation dynamics; it can also be used to model the neural environment of single cells in a multiscale approach.},
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abstract = {Artificial neural networks are usually built on rather few elements such as activation functions, learning rules, and the network topology. When modelling the more complex properties of realistic networks, however, a number of higher-level structural principles become important. In this paper we present a theoretical framework for modelling cortical networks at a high level of abstraction. Based on the notion of a population of neurons, this framework can accommodate the common features of cortical architecture, such as lamination, multiple areas and topographic maps, input segregation, and local variations of the frequency of different cell types (e.g., cytochrome oxidase blobs). The framework is meant primarily for the simulation of activation dynamics; it can also be used to model the neural environment of single cells in a multiscale approach.},
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keywords = {Animals; Cerebral Cortex; Cybernetics; Feedback; Humans; Mathematics; Models, Neurological; Nerve Net; Neural Networks, Computer; Thalamus; Visual Cortex; },
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keywords = {Animals; Cerebral Cortex; Cybernetics; Feedback; Humans; Mathematics; Models, Neurological; Nerve Net; Neural Networks, Computer; Thalamus; Visual Cortex; },
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pubmed = {9008348},
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pmid = {9008348},
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doi = {10.1007/s004220050309},
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doi = {10.1007/s004220050309},
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url = {papers/Mallot_BiolCybern1996-9008348.pdf},
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url = {papers/Mallot_BiolCybern1996-9008348.pdf},
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nlmuniqueid = {7502533}
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nlmuniqueid = {7502533}
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@@ -112923,7 +112958,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
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pages = {1116-33},
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pages = {1116-33},
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abstract = {The intrinsic connections of the cortex have long been known to run vertically, across the cortical layers. In the present study we have found that individual neurons in the cat primary visual cortex can communicate over suprisingly long distances horizontally (up to 4 mm), in directions parallel to the cortical surface. For all of the cells having widespread projections, the collaterals within their axonal fields were distributed in repeating clusters, with an average periodicity of 1 mm. This pattern of extensive clustered projections has been revealed by combining the techniques of intracellular recording and injection of horseradish peroxidase with three-dimensional computer graphic reconstructions. The clustering pattern was most apparent when the cells were rotated to present a view parallel to the cortical surface. The pattern was observed in more than half of the pyramidal and spiny stellate cells in the cortex and was seen in all cortical layers. In our sample, cells made distant connections within their own layer and/or within another layer. The axon of one cell had clusters covering the same area in two layers, and the clusters in the deeper layer were located under those in the upper layer, suggesting a relationship between the clustering phenomenon and columnar cortical architecture. Some pyramidal cells did not project into the white matter, forming intrinsic connections exclusively. Finally, the axonal fields of all our injected cells were asymmetric, extending for greater distances along one cortical axis than along the orthogonal axis. The axons appeared to cover areas of cortex representing a larger part of the visual field than that covered by the excitatory portion of the cell's own receptive field. These connections may be used to generate larger receptive fields or to produce the inhibitory flanks in other cells' receptive fields.},
|
abstract = {The intrinsic connections of the cortex have long been known to run vertically, across the cortical layers. In the present study we have found that individual neurons in the cat primary visual cortex can communicate over suprisingly long distances horizontally (up to 4 mm), in directions parallel to the cortical surface. For all of the cells having widespread projections, the collaterals within their axonal fields were distributed in repeating clusters, with an average periodicity of 1 mm. This pattern of extensive clustered projections has been revealed by combining the techniques of intracellular recording and injection of horseradish peroxidase with three-dimensional computer graphic reconstructions. The clustering pattern was most apparent when the cells were rotated to present a view parallel to the cortical surface. The pattern was observed in more than half of the pyramidal and spiny stellate cells in the cortex and was seen in all cortical layers. In our sample, cells made distant connections within their own layer and/or within another layer. The axon of one cell had clusters covering the same area in two layers, and the clusters in the deeper layer were located under those in the upper layer, suggesting a relationship between the clustering phenomenon and columnar cortical architecture. Some pyramidal cells did not project into the white matter, forming intrinsic connections exclusively. Finally, the axonal fields of all our injected cells were asymmetric, extending for greater distances along one cortical axis than along the orthogonal axis. The axons appeared to cover areas of cortex representing a larger part of the visual field than that covered by the excitatory portion of the cell's own receptive field. These connections may be used to generate larger receptive fields or to produce the inhibitory flanks in other cells' receptive fields.},
|
||||||
keywords = {Animals; Axonal Transport; Cats; Horseradish Peroxidase; Pyramidal Tracts; Visual Cortex; },
|
keywords = {Animals; Axonal Transport; Cats; Horseradish Peroxidase; Pyramidal Tracts; Visual Cortex; },
|
||||||
pubmed = {6188819},
|
pmid = {6188819},
|
||||||
pmc = {PMC6564507},
|
pmc = {PMC6564507},
|
||||||
url = {papers/Gilbert_JNeurosci1983-6188819.pdf},
|
url = {papers/Gilbert_JNeurosci1983-6188819.pdf},
|
||||||
nlmuniqueid = {8102140}
|
nlmuniqueid = {8102140}
|
||||||
@@ -112940,7 +112975,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {1-2},
|
pages = {1-2},
|
||||||
abstract = {The Wilson-Cowan model of interacting neurons (1973) is one of the most influential papers published in Biological Cybernetics (Kybernetik). This paper and a companion paper published in 1972 have been cited over 1000 times. Rather than focus on the microscopic properties of neurons, Wilson and Cowan analyzed the collective properties of large numbers of neurons using methods from statistical mechanics, based on the mean-field approach. New experimental techniques to measure neuronal activity at the level of large populations are now available to test these models, including optical recording of brain activity with intrinsic signals and voltage sensitive dyes, and new methods for analyzing EEG and MEG. These measurement techniques have revealed patterns of coherent activity that span centimetres of tissue in the cerebral cortex. Here the underlying ideas are reviewed in a historic context.},
|
abstract = {The Wilson-Cowan model of interacting neurons (1973) is one of the most influential papers published in Biological Cybernetics (Kybernetik). This paper and a companion paper published in 1972 have been cited over 1000 times. Rather than focus on the microscopic properties of neurons, Wilson and Cowan analyzed the collective properties of large numbers of neurons using methods from statistical mechanics, based on the mean-field approach. New experimental techniques to measure neuronal activity at the level of large populations are now available to test these models, including optical recording of brain activity with intrinsic signals and voltage sensitive dyes, and new methods for analyzing EEG and MEG. These measurement techniques have revealed patterns of coherent activity that span centimetres of tissue in the cerebral cortex. Here the underlying ideas are reviewed in a historic context.},
|
||||||
keywords = {Animals; Humans; Models, Neurological; Nerve Net; Neurons; },
|
keywords = {Animals; Humans; Models, Neurological; Nerve Net; Neurons; },
|
||||||
pubmed = {19662434},
|
pmid = {19662434},
|
||||||
doi = {10.1007/s00422-009-0328-3},
|
doi = {10.1007/s00422-009-0328-3},
|
||||||
pmc = {PMC2866289},
|
pmc = {PMC2866289},
|
||||||
mid = {HHMIMS199370},
|
mid = {HHMIMS199370},
|
||||||
@@ -112959,7 +112994,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {1689-1705},
|
pages = {1689-1705},
|
||||||
abstract = {Maximal longevity of endotherms has long been considered to increase with decreasing specific metabolic rate, and thus with increasing body mass. Using a dataset of over 700 species, here I show that maximal longevity, age at sexual maturity, and postmaturity longevity across bird and mammalian species instead correlate primarily, and universally, with the number of cortical brain neurons. Correlations with metabolic rate and body mass are entirely explained by clade-specific relationships between these variables and numbers of cortical neurons across species. Importantly, humans reach sexual maturity and subsequently live just as long as expected for their number of cortical neurons, which eliminates the basis for earlier theories of protracted childhood and prolonged post-menopause longevity as derived human characteristics. Longevity might increase together with numbers of cortical neurons through their impact on three main factors: delay of sexual maturity, which postpones the onset of aging; lengthening of the period of viable physiological integration and adaptation, which increases postmaturity longevity; and improved cognitive capabilities that benefit survival of the self and of longer-lived progeny, and are conducive to prolonged learning and cultural transmission through increased generational overlap. Importantly, the findings indicate that theories of aging and neurodegenerative diseases should take absolute time lived besides relative "age" into consideration.},
|
abstract = {Maximal longevity of endotherms has long been considered to increase with decreasing specific metabolic rate, and thus with increasing body mass. Using a dataset of over 700 species, here I show that maximal longevity, age at sexual maturity, and postmaturity longevity across bird and mammalian species instead correlate primarily, and universally, with the number of cortical brain neurons. Correlations with metabolic rate and body mass are entirely explained by clade-specific relationships between these variables and numbers of cortical neurons across species. Importantly, humans reach sexual maturity and subsequently live just as long as expected for their number of cortical neurons, which eliminates the basis for earlier theories of protracted childhood and prolonged post-menopause longevity as derived human characteristics. Longevity might increase together with numbers of cortical neurons through their impact on three main factors: delay of sexual maturity, which postpones the onset of aging; lengthening of the period of viable physiological integration and adaptation, which increases postmaturity longevity; and improved cognitive capabilities that benefit survival of the self and of longer-lived progeny, and are conducive to prolonged learning and cultural transmission through increased generational overlap. Importantly, the findings indicate that theories of aging and neurodegenerative diseases should take absolute time lived besides relative "age" into consideration.},
|
||||||
keywords = {AnAge; body size; cerebral cortex; longevity; metabolic rate; number of neurons; scaling; sexual maturity; Aging; Animals; Cerebral Cortex; Female; Humans; Longevity; Male; Neurons; Sexual Maturation; Species Specificity; },
|
keywords = {AnAge; body size; cerebral cortex; longevity; metabolic rate; number of neurons; scaling; sexual maturity; Aging; Animals; Cerebral Cortex; Female; Humans; Longevity; Male; Neurons; Sexual Maturation; Species Specificity; },
|
||||||
pubmed = {30350858},
|
pmid = {30350858},
|
||||||
doi = {10.1002/cne.24564},
|
doi = {10.1002/cne.24564},
|
||||||
url = {papers/Herculano-Houzel_JCompNeurol2019-30350858.pdf},
|
url = {papers/Herculano-Houzel_JCompNeurol2019-30350858.pdf},
|
||||||
nlmuniqueid = {0406041}
|
nlmuniqueid = {0406041}
|
||||||
@@ -112975,7 +113010,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
month = {May},
|
month = {May},
|
||||||
pages = {4160-4168},
|
pages = {4160-4168},
|
||||||
abstract = {The brain functions through coordinated activity among distributed regions. Wide-field calcium imaging, combined with improved genetically encoded calcium indicators, allows sufficient signal-to-noise ratio and spatiotemporal resolution to afford a unique opportunity to capture cortex-wide dynamics on a moment-by-moment basis in behaving animals. Recent applications of this approach have been uncovering cortical dynamics at unprecedented scales during various cognitive processes, ranging from relatively simple sensorimotor integration to more complex decision-making tasks. In this review, we will highlight recent scientific advances enabled by wide-field calcium imaging in behaving mice. We then summarize several technical considerations and future opportunities for wide-field imaging to uncover large-scale circuit dynamics.},
|
abstract = {The brain functions through coordinated activity among distributed regions. Wide-field calcium imaging, combined with improved genetically encoded calcium indicators, allows sufficient signal-to-noise ratio and spatiotemporal resolution to afford a unique opportunity to capture cortex-wide dynamics on a moment-by-moment basis in behaving animals. Recent applications of this approach have been uncovering cortical dynamics at unprecedented scales during various cognitive processes, ranging from relatively simple sensorimotor integration to more complex decision-making tasks. In this review, we will highlight recent scientific advances enabled by wide-field calcium imaging in behaving mice. We then summarize several technical considerations and future opportunities for wide-field imaging to uncover large-scale circuit dynamics.},
|
||||||
pubmed = {33893217},
|
pmid = {33893217},
|
||||||
pii = {JNEUROSCI.3003-20.2021},
|
pii = {JNEUROSCI.3003-20.2021},
|
||||||
doi = {10.1523/JNEUROSCI.3003-20.2021},
|
doi = {10.1523/JNEUROSCI.3003-20.2021},
|
||||||
url = {papers/Ren_JNeurosci2021-33893217.pdf},
|
url = {papers/Ren_JNeurosci2021-33893217.pdf},
|
||||||
@@ -112991,7 +113026,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
year = {2014},
|
year = {2014},
|
||||||
pages = {132},
|
pages = {132},
|
||||||
abstract = {Possessing large brains and complex behavioral patterns, cetaceans are believed to be highly intelligent. Their brains, which are the largest in the Animal Kingdom and have enormous gyrification compared with terrestrial mammals, have long been of scientific interest. Few studies, however, report total number of brain cells in cetaceans, and even fewer have used unbiased counting methods. In this study, using stereological methods, we estimated the total number of cells in the neocortex of the long-finned pilot whale (Globicephala melas) brain. For the first time, we show that a species of dolphin has more neocortical neurons than any mammal studied to date including humans. These cell numbers are compared across various mammals with different brain sizes, and the function of possessing many neurons is discussed. We found that the long-finned pilot whale neocortex has approximately 37.2 × 10(9) neurons, which is almost twice as many as humans, and 127 × 10(9) glial cells. Thus, the absolute number of neurons in the human neocortex is not correlated with the superior cognitive abilities of humans (at least compared to cetaceans) as has previously been hypothesized. However, as neuron density in long-finned pilot whales is lower than that in humans, their higher cell number appears to be due to their larger brain. Accordingly, our findings make an important contribution to the ongoing debate over quantitative relationships in the mammalian brain. },
|
abstract = {Possessing large brains and complex behavioral patterns, cetaceans are believed to be highly intelligent. Their brains, which are the largest in the Animal Kingdom and have enormous gyrification compared with terrestrial mammals, have long been of scientific interest. Few studies, however, report total number of brain cells in cetaceans, and even fewer have used unbiased counting methods. In this study, using stereological methods, we estimated the total number of cells in the neocortex of the long-finned pilot whale (Globicephala melas) brain. For the first time, we show that a species of dolphin has more neocortical neurons than any mammal studied to date including humans. These cell numbers are compared across various mammals with different brain sizes, and the function of possessing many neurons is discussed. We found that the long-finned pilot whale neocortex has approximately 37.2 × 10(9) neurons, which is almost twice as many as humans, and 127 × 10(9) glial cells. Thus, the absolute number of neurons in the human neocortex is not correlated with the superior cognitive abilities of humans (at least compared to cetaceans) as has previously been hypothesized. However, as neuron density in long-finned pilot whales is lower than that in humans, their higher cell number appears to be due to their larger brain. Accordingly, our findings make an important contribution to the ongoing debate over quantitative relationships in the mammalian brain. },
|
||||||
pubmed = {25505387},
|
pmid = {25505387},
|
||||||
doi = {10.3389/fnana.2014.00132},
|
doi = {10.3389/fnana.2014.00132},
|
||||||
pmc = {PMC4244864},
|
pmc = {PMC4244864},
|
||||||
url = {papers/Mortensen_FrontNeuroanat2014-25505387.pdf},
|
url = {papers/Mortensen_FrontNeuroanat2014-25505387.pdf},
|
||||||
@@ -113008,7 +113043,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {145-63},
|
pages = {145-63},
|
||||||
abstract = {Comparative studies amongst extant species are one of the pillars of evolutionary neurobiology. In the 20th century, most comparative studies remained restricted to analyses of brain structure volume and surface areas, besides estimates of neuronal density largely limited to the cerebral cortex. Over the last 10 years, we have amassed data on the numbers of neurons and other cells that compose the entirety of the brain (subdivided into cerebral cortex, cerebellum, and rest of brain) of 39 mammalian species spread over 6 clades, as well as their densities. Here we provide that entire dataset in a format that is readily useful to researchers of any area of interest in the hope that it will foster the advancement of evolutionary and comparative studies well beyond the scope of neuroscience itself. We also reexamine the relationship between numbers of neurons, neuronal densities and body mass, and find that in the rest of brain, but not in the cerebral cortex or cerebellum, there is a single scaling rule that applies to average neuronal cell size, which increases with the linear dimension of the body, even though there is no single scaling rule that relates the number of neurons in the rest of brain to body mass. Thus, larger bodies do not uniformly come with more neurons--but they do fairly uniformly come with larger neurons in the rest of brain, which contains a number of structures directly connected to sources or targets in the body.},
|
abstract = {Comparative studies amongst extant species are one of the pillars of evolutionary neurobiology. In the 20th century, most comparative studies remained restricted to analyses of brain structure volume and surface areas, besides estimates of neuronal density largely limited to the cerebral cortex. Over the last 10 years, we have amassed data on the numbers of neurons and other cells that compose the entirety of the brain (subdivided into cerebral cortex, cerebellum, and rest of brain) of 39 mammalian species spread over 6 clades, as well as their densities. Here we provide that entire dataset in a format that is readily useful to researchers of any area of interest in the hope that it will foster the advancement of evolutionary and comparative studies well beyond the scope of neuroscience itself. We also reexamine the relationship between numbers of neurons, neuronal densities and body mass, and find that in the rest of brain, but not in the cerebral cortex or cerebellum, there is a single scaling rule that applies to average neuronal cell size, which increases with the linear dimension of the body, even though there is no single scaling rule that relates the number of neurons in the rest of brain to body mass. Thus, larger bodies do not uniformly come with more neurons--but they do fairly uniformly come with larger neurons in the rest of brain, which contains a number of structures directly connected to sources or targets in the body.},
|
||||||
keywords = {Animals; Artiodactyla; Biological Evolution; Body Size; Brain; Cell Count; Cell Size; Mammals; Neuroglia; Neurons; Primates; Scandentia; },
|
keywords = {Animals; Artiodactyla; Biological Evolution; Body Size; Brain; Cell Count; Cell Size; Mammals; Neuroglia; Neurons; Primates; Scandentia; },
|
||||||
pubmed = {26418466},
|
pmid = {26418466},
|
||||||
pii = {000437413},
|
pii = {000437413},
|
||||||
doi = {10.1159/000437413},
|
doi = {10.1159/000437413},
|
||||||
url = {papers/Herculano-Houzel_BrainBehavEvol2015-26418466.pdf},
|
url = {papers/Herculano-Houzel_BrainBehavEvol2015-26418466.pdf},
|
||||||
@@ -113026,7 +113061,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {740-5},
|
pages = {740-5},
|
||||||
abstract = {The density of cells and neurons in the neocortex of many mammals varies across cortical areas and regions. This variability is, perhaps, most pronounced in primates. Nonuniformity in the composition of cortex suggests regions of the cortex have different specializations. Specifically, regions with densely packed neurons contain smaller neurons that are activated by relatively few inputs, thereby preserving information, whereas regions that are less densely packed have larger neurons that have more integrative functions. Here we present the numbers of cells and neurons for 742 discrete locations across the neocortex in a chimpanzee. Using isotropic fractionation and flow fractionation methods for cell and neuron counts, we estimate that neocortex of one hemisphere contains 9.5 billion cells and 3.7 billion neurons. Primary visual cortex occupies 35 cm(2) of surface, 10% of the total, and contains 737 million densely packed neurons, 20% of the total neurons contained within the hemisphere. Other areas of high neuron packing include secondary visual areas, somatosensory cortex, and prefrontal granular cortex. Areas of low levels of neuron packing density include motor and premotor cortex. These values reflect those obtained from more limited samples of cortex in humans and other primates. },
|
abstract = {The density of cells and neurons in the neocortex of many mammals varies across cortical areas and regions. This variability is, perhaps, most pronounced in primates. Nonuniformity in the composition of cortex suggests regions of the cortex have different specializations. Specifically, regions with densely packed neurons contain smaller neurons that are activated by relatively few inputs, thereby preserving information, whereas regions that are less densely packed have larger neurons that have more integrative functions. Here we present the numbers of cells and neurons for 742 discrete locations across the neocortex in a chimpanzee. Using isotropic fractionation and flow fractionation methods for cell and neuron counts, we estimate that neocortex of one hemisphere contains 9.5 billion cells and 3.7 billion neurons. Primary visual cortex occupies 35 cm(2) of surface, 10% of the total, and contains 737 million densely packed neurons, 20% of the total neurons contained within the hemisphere. Other areas of high neuron packing include secondary visual areas, somatosensory cortex, and prefrontal granular cortex. Areas of low levels of neuron packing density include motor and premotor cortex. These values reflect those obtained from more limited samples of cortex in humans and other primates. },
|
||||||
keywords = {flow fractionator; isotropic fractionator; neuron density; primate neocortex; visual cortex; Aging; Animals; Cell Count; Female; Motor Cortex; Neocortex; Neurons; Pan troglodytes; Somatosensory Cortex; Visual Cortex; },
|
keywords = {flow fractionator; isotropic fractionator; neuron density; primate neocortex; visual cortex; Aging; Animals; Cell Count; Female; Motor Cortex; Neocortex; Neurons; Pan troglodytes; Somatosensory Cortex; Visual Cortex; },
|
||||||
pubmed = {26729880},
|
pmid = {26729880},
|
||||||
pii = {1524208113},
|
pii = {1524208113},
|
||||||
doi = {10.1073/pnas.1524208113},
|
doi = {10.1073/pnas.1524208113},
|
||||||
pmc = {PMC4725503},
|
pmc = {PMC4725503},
|
||||||
@@ -113042,7 +113077,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
year = {2014},
|
year = {2014},
|
||||||
pages = {46},
|
pages = {46},
|
||||||
abstract = {What explains the superior cognitive abilities of the human brain compared to other, larger brains? Here we investigate the possibility that the human brain has a larger number of neurons than even larger brains by determining the cellular composition of the brain of the African elephant. We find that the African elephant brain, which is about three times larger than the human brain, contains 257 billion (10(9)) neurons, three times more than the average human brain; however, 97.5% of the neurons in the elephant brain (251 billion) are found in the cerebellum. This makes the elephant an outlier in regard to the number of cerebellar neurons compared to other mammals, which might be related to sensorimotor specializations. In contrast, the elephant cerebral cortex, which has twice the mass of the human cerebral cortex, holds only 5.6 billion neurons, about one third of the number of neurons found in the human cerebral cortex. This finding supports the hypothesis that the larger absolute number of neurons in the human cerebral cortex (but not in the whole brain) is correlated with the superior cognitive abilities of humans compared to elephants and other large-brained mammals. },
|
abstract = {What explains the superior cognitive abilities of the human brain compared to other, larger brains? Here we investigate the possibility that the human brain has a larger number of neurons than even larger brains by determining the cellular composition of the brain of the African elephant. We find that the African elephant brain, which is about three times larger than the human brain, contains 257 billion (10(9)) neurons, three times more than the average human brain; however, 97.5% of the neurons in the elephant brain (251 billion) are found in the cerebellum. This makes the elephant an outlier in regard to the number of cerebellar neurons compared to other mammals, which might be related to sensorimotor specializations. In contrast, the elephant cerebral cortex, which has twice the mass of the human cerebral cortex, holds only 5.6 billion neurons, about one third of the number of neurons found in the human cerebral cortex. This finding supports the hypothesis that the larger absolute number of neurons in the human cerebral cortex (but not in the whole brain) is correlated with the superior cognitive abilities of humans compared to elephants and other large-brained mammals. },
|
||||||
pubmed = {24971054},
|
pmid = {24971054},
|
||||||
doi = {10.3389/fnana.2014.00046},
|
doi = {10.3389/fnana.2014.00046},
|
||||||
pmc = {PMC4053853},
|
pmc = {PMC4053853},
|
||||||
url = {papers/Herculano-Houzel_FrontNeuroanat2014-24971054.pdf},
|
url = {papers/Herculano-Houzel_FrontNeuroanat2014-24971054.pdf},
|
||||||
@@ -113061,7 +113096,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {274-282.e6},
|
pages = {274-282.e6},
|
||||||
abstract = {Single-cell transcriptomics of neocortical neurons have revealed more than 100 clusters corresponding to putative cell types. For inhibitory and subcortical projection neurons (SCPNs), there is a strong concordance between clusters and anatomical descriptions of cell types. In contrast, cortico-cortical projection neurons (CCPNs) separate into surprisingly few transcriptomic clusters, despite their diverse anatomical projection types. We used projection-dependent single-cell transcriptomic analyses and monosynaptic rabies tracing to compare mouse primary visual cortex CCPNs projecting to different higher visual areas. We find that layer 2/3 CCPNs with different anatomical projections differ systematically in their gene expressions, despite forming only a single genetic cluster. Furthermore, these neurons receive feedback selectively from the same areas to which they project. These findings demonstrate that gene-expression analysis in isolation is insufficient to identify neuron types and have important implications for understanding the functional role of cortical feedback circuits.},
|
abstract = {Single-cell transcriptomics of neocortical neurons have revealed more than 100 clusters corresponding to putative cell types. For inhibitory and subcortical projection neurons (SCPNs), there is a strong concordance between clusters and anatomical descriptions of cell types. In contrast, cortico-cortical projection neurons (CCPNs) separate into surprisingly few transcriptomic clusters, despite their diverse anatomical projection types. We used projection-dependent single-cell transcriptomic analyses and monosynaptic rabies tracing to compare mouse primary visual cortex CCPNs projecting to different higher visual areas. We find that layer 2/3 CCPNs with different anatomical projections differ systematically in their gene expressions, despite forming only a single genetic cluster. Furthermore, these neurons receive feedback selectively from the same areas to which they project. These findings demonstrate that gene-expression analysis in isolation is insufficient to identify neuron types and have important implications for understanding the functional role of cortical feedback circuits.},
|
||||||
keywords = {cell types; connectivity; cortico-cortical projection neurons; feedback circuits; rabies tracing; single-cell RNA sequencing; visual cortex; Animals; Cerebral Cortex; Feedback; Female; Gene Expression; Gene Knock-In Techniques; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Neocortex; Nerve Net; Neural Pathways; Neurons; Rabies virus; Transcriptome; Visual Cortex; },
|
keywords = {cell types; connectivity; cortico-cortical projection neurons; feedback circuits; rabies tracing; single-cell RNA sequencing; visual cortex; Animals; Cerebral Cortex; Feedback; Female; Gene Expression; Gene Knock-In Techniques; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Neocortex; Nerve Net; Neural Pathways; Neurons; Rabies virus; Transcriptome; Visual Cortex; },
|
||||||
pubmed = {32396852},
|
pmid = {32396852},
|
||||||
pii = {S0896-6273(20)30310-X},
|
pii = {S0896-6273(20)30310-X},
|
||||||
doi = {10.1016/j.neuron.2020.04.018},
|
doi = {10.1016/j.neuron.2020.04.018},
|
||||||
pmc = {PMC7381365},
|
pmc = {PMC7381365},
|
||||||
@@ -113080,7 +113115,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
month = {Sep},
|
month = {Sep},
|
||||||
pages = {37-60},
|
pages = {37-60},
|
||||||
abstract = {Impedance and potential measurements have been made on a number of artificial membranes. Impedance changes were determined as functions of current and of the composition of the environmental solutions. It was shown that rectification is present in asymmetrical systems and that it increases with the membrane potential. The behavior in pairs of solutions of the same salt at different concentrations has formed the basis for the studies although a few experiments with different salts at the same concentrations gave results consistent with the conclusions drawn. A theoretical picture has been presented based on the use of the general kinetic equations for ion motion under the influence of diffusion and electrical forces and on a consideration of possible membrane structures. The equations have been solved for two very simple cases; one based on the assumption of microscopic electroneutrality, and the other on the assumption of a constant electric field. The latter was found to give better results than the former in interpreting the data on potentials and rectification, showing agreement, however, of the right order of magnitude only. Although the indications are that a careful treatment of boundary conditions may result in better agreement with experiment, no attempt has been made to carry this through since the data now available are not sufficiently complete or reproducible. Applications of the second theoretical case to the squid giant axon have been made showing qualitative agreement with the rectification properties and very good agreement with the membrane potential data.},
|
abstract = {Impedance and potential measurements have been made on a number of artificial membranes. Impedance changes were determined as functions of current and of the composition of the environmental solutions. It was shown that rectification is present in asymmetrical systems and that it increases with the membrane potential. The behavior in pairs of solutions of the same salt at different concentrations has formed the basis for the studies although a few experiments with different salts at the same concentrations gave results consistent with the conclusions drawn. A theoretical picture has been presented based on the use of the general kinetic equations for ion motion under the influence of diffusion and electrical forces and on a consideration of possible membrane structures. The equations have been solved for two very simple cases; one based on the assumption of microscopic electroneutrality, and the other on the assumption of a constant electric field. The latter was found to give better results than the former in interpreting the data on potentials and rectification, showing agreement, however, of the right order of magnitude only. Although the indications are that a careful treatment of boundary conditions may result in better agreement with experiment, no attempt has been made to carry this through since the data now available are not sufficiently complete or reproducible. Applications of the second theoretical case to the squid giant axon have been made showing qualitative agreement with the rectification properties and very good agreement with the membrane potential data.},
|
||||||
pubmed = {19873371},
|
pmid = {19873371},
|
||||||
doi = {10.1085/jgp.27.1.37},
|
doi = {10.1085/jgp.27.1.37},
|
||||||
url = {papers/Goldman_JGenPhysiol1943-19873371.pdf},
|
url = {papers/Goldman_JGenPhysiol1943-19873371.pdf},
|
||||||
nlmuniqueid = {2985110R}
|
nlmuniqueid = {2985110R}
|
||||||
@@ -113110,7 +113145,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
month = {Apr},
|
month = {Apr},
|
||||||
pages = {218-23},
|
pages = {218-23},
|
||||||
keywords = {Chemical Phenomena; Chemistry, Physical; Ions; Mathematics; Membranes; Permeability; },
|
keywords = {Chemical Phenomena; Chemistry, Physical; Ions; Mathematics; Membranes; Permeability; },
|
||||||
pubmed = {5045041},
|
pmid = {5045041},
|
||||||
url = {},
|
url = {},
|
||||||
nlmuniqueid = {0376521}
|
nlmuniqueid = {0376521}
|
||||||
}
|
}
|
||||||
@@ -113125,7 +113160,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
month = {Jun},
|
month = {Jun},
|
||||||
pages = {629-36},
|
pages = {629-36},
|
||||||
abstract = {The cold dark matter model has become the leading theoretical picture for the formation of structure in the Universe. This model, together with the theory of cosmic inflation, makes a clear prediction for the initial conditions for structure formation and predicts that structures grow hierarchically through gravitational instability. Testing this model requires that the precise measurements delivered by galaxy surveys can be compared to robust and equally precise theoretical calculations. Here we present a simulation of the growth of dark matter structure using 2,160(3) particles, following them from redshift z = 127 to the present in a cube-shaped region 2.230 billion lightyears on a side. In postprocessing, we also follow the formation and evolution of the galaxies and quasars. We show that baryon-induced features in the initial conditions of the Universe are reflected in distorted form in the low-redshift galaxy distribution, an effect that can be used to constrain the nature of dark energy with future generations of observational surveys of galaxies.},
|
abstract = {The cold dark matter model has become the leading theoretical picture for the formation of structure in the Universe. This model, together with the theory of cosmic inflation, makes a clear prediction for the initial conditions for structure formation and predicts that structures grow hierarchically through gravitational instability. Testing this model requires that the precise measurements delivered by galaxy surveys can be compared to robust and equally precise theoretical calculations. Here we present a simulation of the growth of dark matter structure using 2,160(3) particles, following them from redshift z = 127 to the present in a cube-shaped region 2.230 billion lightyears on a side. In postprocessing, we also follow the formation and evolution of the galaxies and quasars. We show that baryon-induced features in the initial conditions of the Universe are reflected in distorted form in the low-redshift galaxy distribution, an effect that can be used to constrain the nature of dark energy with future generations of observational surveys of galaxies.},
|
||||||
pubmed = {15931216},
|
pmid = {15931216},
|
||||||
pii = {nature03597},
|
pii = {nature03597},
|
||||||
doi = {10.1038/nature03597},
|
doi = {10.1038/nature03597},
|
||||||
url = {papers/Springel_Nature2005-15931216.pdf},
|
url = {papers/Springel_Nature2005-15931216.pdf},
|
||||||
@@ -113142,7 +113177,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {26-38},
|
pages = {26-38},
|
||||||
abstract = {Recent advances in genetically engineered calcium and membrane potential indicators provide the potential to estimate the activation dynamics of individual neurons within larger, mesoscale networks (100s-1000+neurons). However, a fully integrated automated workflow for the analysis and visualization of neural microcircuits from high speed fluorescence imaging data is lacking.},
|
abstract = {Recent advances in genetically engineered calcium and membrane potential indicators provide the potential to estimate the activation dynamics of individual neurons within larger, mesoscale networks (100s-1000+neurons). However, a fully integrated automated workflow for the analysis and visualization of neural microcircuits from high speed fluorescence imaging data is lacking.},
|
||||||
keywords = {Calcium imaging; Event detection; FluoroSNNAP; Functional connectivity; Neuronal phenotype; Synchrony; Access to Information; Algorithms; Animals; Calcium; Cells, Cultured; Hippocampus; Humans; Mice, Transgenic; Mutation; Neocortex; Neural Pathways; Neurons; Optical Imaging; Pattern Recognition, Automated; Periodicity; Rats, Sprague-Dawley; Single-Cell Analysis; Software; Wavelet Analysis; tau Proteins; },
|
keywords = {Calcium imaging; Event detection; FluoroSNNAP; Functional connectivity; Neuronal phenotype; Synchrony; Access to Information; Algorithms; Animals; Calcium; Cells, Cultured; Hippocampus; Humans; Mice, Transgenic; Mutation; Neocortex; Neural Pathways; Neurons; Optical Imaging; Pattern Recognition, Automated; Periodicity; Rats, Sprague-Dawley; Single-Cell Analysis; Software; Wavelet Analysis; tau Proteins; },
|
||||||
pubmed = {25629800},
|
pmid = {25629800},
|
||||||
pii = {S0165-0270(15)00021-7},
|
pii = {S0165-0270(15)00021-7},
|
||||||
doi = {10.1016/j.jneumeth.2015.01.020},
|
doi = {10.1016/j.jneumeth.2015.01.020},
|
||||||
pmc = {PMC5553047},
|
pmc = {PMC5553047},
|
||||||
@@ -113162,7 +113197,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {285-99},
|
pages = {285-99},
|
||||||
abstract = {We present a modular approach for analyzing calcium imaging recordings of large neuronal ensembles. Our goal is to simultaneously identify the locations of the neurons, demix spatially overlapping components, and denoise and deconvolve the spiking activity from the slow dynamics of the calcium indicator. Our approach relies on a constrained nonnegative matrix factorization that expresses the spatiotemporal fluorescence activity as the product of a spatial matrix that encodes the spatial footprint of each neuron in the optical field and a temporal matrix that characterizes the calcium concentration of each neuron over time. This framework is combined with a novel constrained deconvolution approach that extracts estimates of neural activity from fluorescence traces, to create a spatiotemporal processing algorithm that requires minimal parameter tuning. We demonstrate the general applicability of our method by applying it to in vitro and in vivo multi-neuronal imaging data, whole-brain light-sheet imaging data, and dendritic imaging data. },
|
abstract = {We present a modular approach for analyzing calcium imaging recordings of large neuronal ensembles. Our goal is to simultaneously identify the locations of the neurons, demix spatially overlapping components, and denoise and deconvolve the spiking activity from the slow dynamics of the calcium indicator. Our approach relies on a constrained nonnegative matrix factorization that expresses the spatiotemporal fluorescence activity as the product of a spatial matrix that encodes the spatial footprint of each neuron in the optical field and a temporal matrix that characterizes the calcium concentration of each neuron over time. This framework is combined with a novel constrained deconvolution approach that extracts estimates of neural activity from fluorescence traces, to create a spatiotemporal processing algorithm that requires minimal parameter tuning. We demonstrate the general applicability of our method by applying it to in vitro and in vivo multi-neuronal imaging data, whole-brain light-sheet imaging data, and dendritic imaging data. },
|
||||||
keywords = {Action Potentials; Animals; Calcium; Dendrites; Fluorescent Dyes; Mice; Mice, Inbred C57BL; Microscopy, Fluorescence; Neurons; Statistics as Topic; },
|
keywords = {Action Potentials; Animals; Calcium; Dendrites; Fluorescent Dyes; Mice; Mice, Inbred C57BL; Microscopy, Fluorescence; Neurons; Statistics as Topic; },
|
||||||
pubmed = {26774160},
|
pmid = {26774160},
|
||||||
pii = {S0896-6273(15)01084-3},
|
pii = {S0896-6273(15)01084-3},
|
||||||
doi = {10.1016/j.neuron.2015.11.037},
|
doi = {10.1016/j.neuron.2015.11.037},
|
||||||
pmc = {PMC4881387},
|
pmc = {PMC4881387},
|
||||||
@@ -113182,7 +113217,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {171-178},
|
pages = {171-178},
|
||||||
abstract = {Understanding the amazingly complex human cerebral cortex requires a map (or parcellation) of its major subdivisions, known as cortical areas. Making an accurate areal map has been a century-old objective in neuroscience. Using multi-modal magnetic resonance images from the Human Connectome Project (HCP) and an objective semi-automated neuroanatomical approach, we delineated 180 areas per hemisphere bounded by sharp changes in cortical architecture, function, connectivity, and/or topography in a precisely aligned group average of 210 healthy young adults. We characterized 97 new areas and 83 areas previously reported using post-mortem microscopy or other specialized study-specific approaches. To enable automated delineation and identification of these areas in new HCP subjects and in future studies, we trained a machine-learning classifier to recognize the multi-modal 'fingerprint' of each cortical area. This classifier detected the presence of 96.6% of the cortical areas in new subjects, replicated the group parcellation, and could correctly locate areas in individuals with atypical parcellations. The freely available parcellation and classifier will enable substantially improved neuroanatomical precision for studies of the structural and functional organization of human cerebral cortex and its variation across individuals and in development, aging, and disease.},
|
abstract = {Understanding the amazingly complex human cerebral cortex requires a map (or parcellation) of its major subdivisions, known as cortical areas. Making an accurate areal map has been a century-old objective in neuroscience. Using multi-modal magnetic resonance images from the Human Connectome Project (HCP) and an objective semi-automated neuroanatomical approach, we delineated 180 areas per hemisphere bounded by sharp changes in cortical architecture, function, connectivity, and/or topography in a precisely aligned group average of 210 healthy young adults. We characterized 97 new areas and 83 areas previously reported using post-mortem microscopy or other specialized study-specific approaches. To enable automated delineation and identification of these areas in new HCP subjects and in future studies, we trained a machine-learning classifier to recognize the multi-modal 'fingerprint' of each cortical area. This classifier detected the presence of 96.6% of the cortical areas in new subjects, replicated the group parcellation, and could correctly locate areas in individuals with atypical parcellations. The freely available parcellation and classifier will enable substantially improved neuroanatomical precision for studies of the structural and functional organization of human cerebral cortex and its variation across individuals and in development, aging, and disease.},
|
||||||
keywords = {Adult; Cerebral Cortex; Connectome; Female; Healthy Volunteers; Humans; Machine Learning; Male; Models, Anatomic; Multimodal Imaging; Neuroanatomy; Neuroimaging; Probability; Reproducibility of Results; Young Adult; },
|
keywords = {Adult; Cerebral Cortex; Connectome; Female; Healthy Volunteers; Humans; Machine Learning; Male; Models, Anatomic; Multimodal Imaging; Neuroanatomy; Neuroimaging; Probability; Reproducibility of Results; Young Adult; },
|
||||||
pubmed = {27437579},
|
pmid = {27437579},
|
||||||
doi = {10.1038/nature18933},
|
doi = {10.1038/nature18933},
|
||||||
pmc = {PMC4990127},
|
pmc = {PMC4990127},
|
||||||
mid = {EMS68870},
|
mid = {EMS68870},
|
||||||
@@ -113201,7 +113236,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {1121-1135},
|
pages = {1121-1135},
|
||||||
abstract = {Complex animal behaviors are likely built from simpler modules, but their systematic identification in mammals remains a significant challenge. Here we use depth imaging to show that 3D mouse pose dynamics are structured at the sub-second timescale. Computational modeling of these fast dynamics effectively describes mouse behavior as a series of reused and stereotyped modules with defined transition probabilities. We demonstrate this combined 3D imaging and machine learning method can be used to unmask potential strategies employed by the brain to adapt to the environment, to capture both predicted and previously hidden phenotypes caused by genetic or neural manipulations, and to systematically expose the global structure of behavior within an experiment. This work reveals that mouse body language is built from identifiable components and is organized in a predictable fashion; deciphering this language establishes an objective framework for characterizing the influence of environmental cues, genes and neural activity on behavior.},
|
abstract = {Complex animal behaviors are likely built from simpler modules, but their systematic identification in mammals remains a significant challenge. Here we use depth imaging to show that 3D mouse pose dynamics are structured at the sub-second timescale. Computational modeling of these fast dynamics effectively describes mouse behavior as a series of reused and stereotyped modules with defined transition probabilities. We demonstrate this combined 3D imaging and machine learning method can be used to unmask potential strategies employed by the brain to adapt to the environment, to capture both predicted and previously hidden phenotypes caused by genetic or neural manipulations, and to systematically expose the global structure of behavior within an experiment. This work reveals that mouse body language is built from identifiable components and is organized in a predictable fashion; deciphering this language establishes an objective framework for characterizing the influence of environmental cues, genes and neural activity on behavior.},
|
||||||
keywords = {Animals; Behavior, Animal; Computer Simulation; Imaging, Three-Dimensional; Kinesics; Machine Learning; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Optogenetics; },
|
keywords = {Animals; Behavior, Animal; Computer Simulation; Imaging, Three-Dimensional; Kinesics; Machine Learning; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Optogenetics; },
|
||||||
pubmed = {26687221},
|
pmid = {26687221},
|
||||||
pii = {S0896-6273(15)01037-5},
|
pii = {S0896-6273(15)01037-5},
|
||||||
doi = {10.1016/j.neuron.2015.11.031},
|
doi = {10.1016/j.neuron.2015.11.031},
|
||||||
pmc = {PMC4708087},
|
pmc = {PMC4708087},
|
||||||
@@ -113221,7 +113256,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {1545-63},
|
pages = {1545-63},
|
||||||
abstract = {The immature retina generates spontaneous waves of spiking activity that sweep across the ganglion cell layer during a limited period of development before the onset of visual experience. The spatiotemporal patterns encoded in the waves are believed to be instructive for the wiring of functional connections throughout the visual system. However, the ontogeny of retinal waves is still poorly documented as a result of the relatively low resolution of conventional recording techniques. Here, we characterize the spatiotemporal features of mouse retinal waves from birth until eye opening in unprecedented detail using a large-scale, dense, 4096-channel multielectrode array that allowed us to record from the entire neonatal retina at near cellular resolution. We found that early cholinergic waves propagate with random trajectories over large areas with low ganglion cell recruitment. They become slower, smaller and denser when GABAA signalling matures, as occurs beyond postnatal day (P) 7. Glutamatergic influences dominate from P10, coinciding with profound changes in activity dynamics. At this time, waves cease to be random and begin to show repetitive trajectories confined to a few localized hotspots. These hotspots gradually tile the retina with time, and disappear after eye opening. Our observations demonstrate that retinal waves undergo major spatiotemporal changes during ontogeny. Our results support the hypotheses that cholinergic waves guide the refinement of retinal targets and that glutamatergic waves may also support the wiring of retinal receptive fields. },
|
abstract = {The immature retina generates spontaneous waves of spiking activity that sweep across the ganglion cell layer during a limited period of development before the onset of visual experience. The spatiotemporal patterns encoded in the waves are believed to be instructive for the wiring of functional connections throughout the visual system. However, the ontogeny of retinal waves is still poorly documented as a result of the relatively low resolution of conventional recording techniques. Here, we characterize the spatiotemporal features of mouse retinal waves from birth until eye opening in unprecedented detail using a large-scale, dense, 4096-channel multielectrode array that allowed us to record from the entire neonatal retina at near cellular resolution. We found that early cholinergic waves propagate with random trajectories over large areas with low ganglion cell recruitment. They become slower, smaller and denser when GABAA signalling matures, as occurs beyond postnatal day (P) 7. Glutamatergic influences dominate from P10, coinciding with profound changes in activity dynamics. At this time, waves cease to be random and begin to show repetitive trajectories confined to a few localized hotspots. These hotspots gradually tile the retina with time, and disappear after eye opening. Our observations demonstrate that retinal waves undergo major spatiotemporal changes during ontogeny. Our results support the hypotheses that cholinergic waves guide the refinement of retinal targets and that glutamatergic waves may also support the wiring of retinal receptive fields. },
|
||||||
keywords = {Action Potentials; Age Factors; Animals; Animals, Newborn; Cholinergic Neurons; GABAergic Neurons; Glutamic Acid; Light Signal Transduction; Mice, Inbred C57BL; Receptors, GABA-A; Retina; Retinal Neurons; Time Factors; Vision, Ocular; },
|
keywords = {Action Potentials; Age Factors; Animals; Animals, Newborn; Cholinergic Neurons; GABAergic Neurons; Glutamic Acid; Light Signal Transduction; Mice, Inbred C57BL; Receptors, GABA-A; Retina; Retinal Neurons; Time Factors; Vision, Ocular; },
|
||||||
pubmed = {24366261},
|
pmid = {24366261},
|
||||||
pii = {jphysiol.2013.262840},
|
pii = {jphysiol.2013.262840},
|
||||||
doi = {10.1113/jphysiol.2013.262840},
|
doi = {10.1113/jphysiol.2013.262840},
|
||||||
pmc = {PMC3979611},
|
pmc = {PMC3979611},
|
||||||
@@ -113240,7 +113275,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {255-268},
|
pages = {255-268},
|
||||||
abstract = {Multichannel recording technologies have revealed travelling waves of neural activity in multiple sensory, motor and cognitive systems. These waves can be spontaneously generated by recurrent circuits or evoked by external stimuli. They travel along brain networks at multiple scales, transiently modulating spiking and excitability as they pass. Here, we review recent experimental findings that have found evidence for travelling waves at single-area (mesoscopic) and whole-brain (macroscopic) scales. We place these findings in the context of the current theoretical understanding of wave generation and propagation in recurrent networks. During the large low-frequency rhythms of sleep or the relatively desynchronized state of the awake cortex, travelling waves may serve a variety of functions, from long-term memory consolidation to processing of dynamic visual stimuli. We explore new avenues for experimental and computational understanding of the role of spatiotemporal activity patterns in the cortex.},
|
abstract = {Multichannel recording technologies have revealed travelling waves of neural activity in multiple sensory, motor and cognitive systems. These waves can be spontaneously generated by recurrent circuits or evoked by external stimuli. They travel along brain networks at multiple scales, transiently modulating spiking and excitability as they pass. Here, we review recent experimental findings that have found evidence for travelling waves at single-area (mesoscopic) and whole-brain (macroscopic) scales. We place these findings in the context of the current theoretical understanding of wave generation and propagation in recurrent networks. During the large low-frequency rhythms of sleep or the relatively desynchronized state of the awake cortex, travelling waves may serve a variety of functions, from long-term memory consolidation to processing of dynamic visual stimuli. We explore new avenues for experimental and computational understanding of the role of spatiotemporal activity patterns in the cortex.},
|
||||||
keywords = {Animals; Brain Waves; Cerebral Cortex; Computer Simulation; Electroencephalography; Humans; Models, Neurological; Neural Pathways; },
|
keywords = {Animals; Brain Waves; Cerebral Cortex; Computer Simulation; Electroencephalography; Humans; Models, Neurological; Neural Pathways; },
|
||||||
pubmed = {29563572},
|
pmid = {29563572},
|
||||||
pii = {nrn.2018.20},
|
pii = {nrn.2018.20},
|
||||||
doi = {10.1038/nrn.2018.20},
|
doi = {10.1038/nrn.2018.20},
|
||||||
pmc = {PMC5933075},
|
pmc = {PMC5933075},
|
||||||
@@ -113259,7 +113294,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {},
|
pages = {},
|
||||||
abstract = {Fluorescent calcium indicators are often used to investigate neural dynamics, but the relationship between fluorescence and action potentials (APs) remains unclear. Most APs can be detected when the soma almost fills the microscope's field of view, but calcium indicators are used to image populations of neurons, necessitating a large field of view, generating fewer photons per neuron, and compromising AP detection. Here, we characterized the AP-fluorescence transfer function in vivo for 48 layer 2/3 pyramidal neurons in primary visual cortex, with simultaneous calcium imaging and cell-attached recordings from transgenic mice expressing GCaMP6s or GCaMP6f. While most APs were detected under optimal conditions, under conditions typical of population imaging studies, only a minority of 1 AP and 2 AP events were detected (often <10% and ~20-30%, respectively), emphasizing the limits of AP detection under more realistic imaging conditions.},
|
abstract = {Fluorescent calcium indicators are often used to investigate neural dynamics, but the relationship between fluorescence and action potentials (APs) remains unclear. Most APs can be detected when the soma almost fills the microscope's field of view, but calcium indicators are used to image populations of neurons, necessitating a large field of view, generating fewer photons per neuron, and compromising AP detection. Here, we characterized the AP-fluorescence transfer function in vivo for 48 layer 2/3 pyramidal neurons in primary visual cortex, with simultaneous calcium imaging and cell-attached recordings from transgenic mice expressing GCaMP6s or GCaMP6f. While most APs were detected under optimal conditions, under conditions typical of population imaging studies, only a minority of 1 AP and 2 AP events were detected (often <10% and ~20-30%, respectively), emphasizing the limits of AP detection under more realistic imaging conditions.},
|
||||||
keywords = {action potential; calcium imaging; calibration; cell-attached recording; excitatory neurons; genetically encoded calcium indicator; mouse; neuroscience; Action Potentials; Animals; Calcium; Calcium-Binding Proteins; Female; Fluorescent Dyes; Male; Mice; Mice, Transgenic; Microscopy, Fluorescence; Primary Visual Cortex; Pyramidal Cells; },
|
keywords = {action potential; calcium imaging; calibration; cell-attached recording; excitatory neurons; genetically encoded calcium indicator; mouse; neuroscience; Action Potentials; Animals; Calcium; Calcium-Binding Proteins; Female; Fluorescent Dyes; Male; Mice; Mice, Transgenic; Microscopy, Fluorescence; Primary Visual Cortex; Pyramidal Cells; },
|
||||||
pubmed = {33683198},
|
pmid = {33683198},
|
||||||
doi = {10.7554/eLife.51675},
|
doi = {10.7554/eLife.51675},
|
||||||
pii = {51675},
|
pii = {51675},
|
||||||
pmc = {PMC8060029},
|
pmc = {PMC8060029},
|
||||||
@@ -113276,7 +113311,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {1116},
|
pages = {1116},
|
||||||
abstract = {Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×10(7) pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens.},
|
abstract = {Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×10(7) pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens.},
|
||||||
keywords = {Imaging, Three-Dimensional; Light; Lighting; Microscopy; },
|
keywords = {Imaging, Three-Dimensional; Light; Lighting; Microscopy; },
|
||||||
pubmed = {23346373},
|
pmid = {23346373},
|
||||||
doi = {10.1038/srep01116},
|
doi = {10.1038/srep01116},
|
||||||
pmc = {PMC3552285},
|
pmc = {PMC3552285},
|
||||||
url = {papers/Dan_SciRep2013-23346373.pdf},
|
url = {papers/Dan_SciRep2013-23346373.pdf},
|
||||||
@@ -113294,7 +113329,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {e0213924},
|
pages = {e0213924},
|
||||||
abstract = {Visual cortex is organized into discrete sub-regions or areas that are arranged into a hierarchy and serves different functions in the processing of visual information. In retinotopic maps of mouse cortex, there appear to be substantial mouse-to-mouse differences in visual area location, size and shape. Here we quantify the biological variation in the size, shape and locations of 11 visual areas in the mouse, after separating biological variation and measurement noise. We find that there is biological variation in the locations and sizes of visual areas.},
|
abstract = {Visual cortex is organized into discrete sub-regions or areas that are arranged into a hierarchy and serves different functions in the processing of visual information. In retinotopic maps of mouse cortex, there appear to be substantial mouse-to-mouse differences in visual area location, size and shape. Here we quantify the biological variation in the size, shape and locations of 11 visual areas in the mouse, after separating biological variation and measurement noise. We find that there is biological variation in the locations and sizes of visual areas.},
|
||||||
keywords = {Animals; Brain Mapping; Male; Mice; Visual Cortex; Visual Pathways; },
|
keywords = {Animals; Brain Mapping; Male; Mice; Visual Cortex; Visual Pathways; },
|
||||||
pubmed = {31042712},
|
pmid = {31042712},
|
||||||
doi = {10.1371/journal.pone.0213924},
|
doi = {10.1371/journal.pone.0213924},
|
||||||
pii = {PONE-D-18-29482},
|
pii = {PONE-D-18-29482},
|
||||||
pmc = {PMC6493719},
|
pmc = {PMC6493719},
|
||||||
@@ -113313,7 +113348,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {33-43},
|
pages = {33-43},
|
||||||
abstract = {Optical imaging has revolutionized our ability to monitor brain activity, spanning spatial scales from synapses to cells to circuits. Here, we summarize the rapid development and application of mesoscopic imaging, a widefield fluorescence-based approach that balances high spatiotemporal resolution with extraordinarily large fields of view. By leveraging the continued expansion of fluorescent reporters for neuronal activity and novel strategies for indicator expression, mesoscopic analysis enables measurement and correlation of network dynamics with behavioral state and task performance. Moreover, the combination of widefield imaging with cellular resolution methods such as two-photon microscopy and electrophysiology is bridging boundaries between cellular and network analyses. Overall, mesoscopic imaging provides a powerful option in the optical toolbox for investigation of brain function.},
|
abstract = {Optical imaging has revolutionized our ability to monitor brain activity, spanning spatial scales from synapses to cells to circuits. Here, we summarize the rapid development and application of mesoscopic imaging, a widefield fluorescence-based approach that balances high spatiotemporal resolution with extraordinarily large fields of view. By leveraging the continued expansion of fluorescent reporters for neuronal activity and novel strategies for indicator expression, mesoscopic analysis enables measurement and correlation of network dynamics with behavioral state and task performance. Moreover, the combination of widefield imaging with cellular resolution methods such as two-photon microscopy and electrophysiology is bridging boundaries between cellular and network analyses. Overall, mesoscopic imaging provides a powerful option in the optical toolbox for investigation of brain function.},
|
||||||
keywords = {Animals; Brain; Calcium; Humans; Intravital Microscopy; Microscopy, Fluorescence, Multiphoton; Neurons; Optical Imaging; },
|
keywords = {Animals; Brain; Calcium; Humans; Intravital Microscopy; Microscopy, Fluorescence, Multiphoton; Neurons; Optical Imaging; },
|
||||||
pubmed = {33058764},
|
pmid = {33058764},
|
||||||
pii = {S0896-6273(20)30755-8},
|
pii = {S0896-6273(20)30755-8},
|
||||||
doi = {10.1016/j.neuron.2020.09.031},
|
doi = {10.1016/j.neuron.2020.09.031},
|
||||||
pmc = {PMC7577373},
|
pmc = {PMC7577373},
|
||||||
@@ -113333,7 +113368,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {511-524.e5},
|
pages = {511-524.e5},
|
||||||
abstract = {Neurons in the developing auditory system exhibit spontaneous bursts of activity before hearing onset. How this intrinsically generated activity influences development remains uncertain, because few mechanistic studies have been performed in vivo. We show using macroscopic calcium imaging in unanesthetized mice that neurons responsible for processing similar frequencies of sound exhibit highly synchronized activity throughout the auditory system during this critical phase of development. Spontaneous activity normally requires synaptic excitation of spiral ganglion neurons (SGNs). Unexpectedly, tonotopic spontaneous activity was preserved in a mouse model of deafness in which glutamate release from hair cells is abolished. SGNs in these mice exhibited enhanced excitability, enabling direct neuronal excitation by supporting cell-induced potassium transients. These results indicate that homeostatic mechanisms maintain spontaneous activity in the pre-hearing period, with significant implications for both circuit development and therapeutic approaches aimed at treating congenital forms of deafness arising through mutations in key sensory transduction components.},
|
abstract = {Neurons in the developing auditory system exhibit spontaneous bursts of activity before hearing onset. How this intrinsically generated activity influences development remains uncertain, because few mechanistic studies have been performed in vivo. We show using macroscopic calcium imaging in unanesthetized mice that neurons responsible for processing similar frequencies of sound exhibit highly synchronized activity throughout the auditory system during this critical phase of development. Spontaneous activity normally requires synaptic excitation of spiral ganglion neurons (SGNs). Unexpectedly, tonotopic spontaneous activity was preserved in a mouse model of deafness in which glutamate release from hair cells is abolished. SGNs in these mice exhibited enhanced excitability, enabling direct neuronal excitation by supporting cell-induced potassium transients. These results indicate that homeostatic mechanisms maintain spontaneous activity in the pre-hearing period, with significant implications for both circuit development and therapeutic approaches aimed at treating congenital forms of deafness arising through mutations in key sensory transduction components.},
|
||||||
keywords = {Acoustic Stimulation; Animals; Auditory Cortex; Auditory Pathways; Cochlea; Female; Hair Cells, Auditory; Hearing; Homeostasis; Male; Mice; Mice, Transgenic; Random Allocation; Spiral Ganglion; },
|
keywords = {Acoustic Stimulation; Animals; Auditory Cortex; Auditory Pathways; Cochlea; Female; Hair Cells, Auditory; Hearing; Homeostasis; Male; Mice; Mice, Transgenic; Random Allocation; Spiral Ganglion; },
|
||||||
pubmed = {30077356},
|
pmid = {30077356},
|
||||||
pii = {S0896-6273(18)30544-0},
|
pii = {S0896-6273(18)30544-0},
|
||||||
doi = {10.1016/j.neuron.2018.07.004},
|
doi = {10.1016/j.neuron.2018.07.004},
|
||||||
pmc = {PMC6100752},
|
pmc = {PMC6100752},
|
||||||
@@ -113353,7 +113388,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {29212-29220},
|
pages = {29212-29220},
|
||||||
abstract = {While the mechanisms generating the topographic organization of primary sensory areas in the neocortex are well studied, what generates secondary cortical areas is virtually unknown. Using physical parameters representing primary and secondary visual areas as they vary from monkey to mouse, we derived a network growth model to explore if characteristic features of secondary areas could be produced from correlated activity patterns arising from V1 alone. We found that V1 seeded variable numbers of secondary areas based on activity-driven wiring and wiring-density limits within the cortical surface. These secondary areas exhibited the typical mirror-reversal of map topography on cortical area boundaries and progressive reduction of the area and spatial resolution of each new map on the caudorostral axis. Activity-based map formation may be the basic mechanism that establishes the matrix of topographically organized cortical areas available for later computational specialization.},
|
abstract = {While the mechanisms generating the topographic organization of primary sensory areas in the neocortex are well studied, what generates secondary cortical areas is virtually unknown. Using physical parameters representing primary and secondary visual areas as they vary from monkey to mouse, we derived a network growth model to explore if characteristic features of secondary areas could be produced from correlated activity patterns arising from V1 alone. We found that V1 seeded variable numbers of secondary areas based on activity-driven wiring and wiring-density limits within the cortical surface. These secondary areas exhibited the typical mirror-reversal of map topography on cortical area boundaries and progressive reduction of the area and spatial resolution of each new map on the caudorostral axis. Activity-based map formation may be the basic mechanism that establishes the matrix of topographically organized cortical areas available for later computational specialization.},
|
||||||
keywords = {cortical areas; development; evolution; network neuroscience; topographic maps; Animals; Biological Evolution; Brain; Macaca mulatta; Mice; Models, Biological; Neocortex; Nerve Net; Somatosensory Cortex; Visual Cortex; },
|
keywords = {cortical areas; development; evolution; network neuroscience; topographic maps; Animals; Biological Evolution; Brain; Macaca mulatta; Mice; Models, Biological; Neocortex; Nerve Net; Somatosensory Cortex; Visual Cortex; },
|
||||||
pubmed = {33139564},
|
pmid = {33139564},
|
||||||
pii = {2011724117},
|
pii = {2011724117},
|
||||||
doi = {10.1073/pnas.2011724117},
|
doi = {10.1073/pnas.2011724117},
|
||||||
pmc = {PMC7682404},
|
pmc = {PMC7682404},
|
||||||
@@ -113372,7 +113407,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {422-432},
|
pages = {422-432},
|
||||||
abstract = {Grid cells provide a compelling example of a link between cellular activity and an abstract and difficult to define concept like space. Accordingly, a representational perspective on grid coding argues that neural grid coding underlies a fundamentally spatial metric. Recently, some theoretical proposals have suggested extending such a framework to nonspatial cognition as well, such as category learning. Here, we provide a critique of the frequently employed assumption of an isomorphism between patterns of neural activity (e.g., grid cells), mental representation, and behavior (e.g., navigation). Specifically, we question the strict isomorphism between these three levels and suggest that human spatial navigation is perhaps best characterized by a wide variety of both metric and nonmetric strategies. We offer an alternative perspective on how grid coding might relate to human spatial navigation, arguing that grid coding is part of a much larger conglomeration of neural activity patterns that dynamically tune to accomplish specific behavioral outputs.},
|
abstract = {Grid cells provide a compelling example of a link between cellular activity and an abstract and difficult to define concept like space. Accordingly, a representational perspective on grid coding argues that neural grid coding underlies a fundamentally spatial metric. Recently, some theoretical proposals have suggested extending such a framework to nonspatial cognition as well, such as category learning. Here, we provide a critique of the frequently employed assumption of an isomorphism between patterns of neural activity (e.g., grid cells), mental representation, and behavior (e.g., navigation). Specifically, we question the strict isomorphism between these three levels and suggest that human spatial navigation is perhaps best characterized by a wide variety of both metric and nonmetric strategies. We offer an alternative perspective on how grid coding might relate to human spatial navigation, arguing that grid coding is part of a much larger conglomeration of neural activity patterns that dynamically tune to accomplish specific behavioral outputs.},
|
||||||
keywords = {entorhinal cortex; grid cells; heuristics; human behavior; spatial navigation; Animals; Entorhinal Cortex; Grid Cells; Humans; Models, Neurological; Spatial Navigation; },
|
keywords = {entorhinal cortex; grid cells; heuristics; human behavior; spatial navigation; Animals; Entorhinal Cortex; Grid Cells; Humans; Models, Neurological; Spatial Navigation; },
|
||||||
pubmed = {31742364},
|
pmid = {31742364},
|
||||||
doi = {10.1002/hipo.23175},
|
doi = {10.1002/hipo.23175},
|
||||||
pmc = {PMC7409510},
|
pmc = {PMC7409510},
|
||||||
mid = {NIHMS1583182},
|
mid = {NIHMS1583182},
|
||||||
@@ -113391,7 +113426,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {1442-57},
|
pages = {1442-57},
|
||||||
abstract = {Previously, we reported that the expression of cytochrome oxidase in a number of brain stem nuclei exhibited a plateau or reduction at postnatal day (P) 3-4 and a dramatic decrease at P12, against a general increase with age. The present study examined the expression of glutamate, N-methyl-D-aspartate receptor subunit 1 (NMDAR1), GABA, GABAB receptors, glycine receptors, and glutamate receptor subunit 2 (GluR2) in the ventrolateral subnucleus of the solitary tract nucleus, nucleus ambiguus, hypoglossal nucleus, medial accessory olivary nucleus, dorsal motor nucleus of the vagus, and cuneate nucleus, from P2 to P21 in rats. Results showed that 1) the expression of glutamate increased with age in a majority of the nuclei, whereas that of NMDAR1 showed heterogeneity among the nuclei; 2) GABA and GABAB expressions decreased with age, whereas that of glycine receptors increased with age; 3) GluR2 showed two peaks, at P3-4 and P12; and 4) glutamate and NMDAR1 showed a significant reduction, whereas GABA, GABAB receptors, glycine receptors, and GluR2 exhibited a concomitant increase at P12. These features were present but less pronounced in hypoglossal nucleus and dorsal motor nucleus of the vagus and were absent in the cuneate nucleus. These data suggest that brain stem nuclei, directly or indirectly related to respiratory control, share a common developmental trend with the pre-Botzinger complex in having a transient period of imbalance between inhibitory and excitatory drives at P12. During this critical period, the respiratory system may be more vulnerable to excessive exogenous stressors.},
|
abstract = {Previously, we reported that the expression of cytochrome oxidase in a number of brain stem nuclei exhibited a plateau or reduction at postnatal day (P) 3-4 and a dramatic decrease at P12, against a general increase with age. The present study examined the expression of glutamate, N-methyl-D-aspartate receptor subunit 1 (NMDAR1), GABA, GABAB receptors, glycine receptors, and glutamate receptor subunit 2 (GluR2) in the ventrolateral subnucleus of the solitary tract nucleus, nucleus ambiguus, hypoglossal nucleus, medial accessory olivary nucleus, dorsal motor nucleus of the vagus, and cuneate nucleus, from P2 to P21 in rats. Results showed that 1) the expression of glutamate increased with age in a majority of the nuclei, whereas that of NMDAR1 showed heterogeneity among the nuclei; 2) GABA and GABAB expressions decreased with age, whereas that of glycine receptors increased with age; 3) GluR2 showed two peaks, at P3-4 and P12; and 4) glutamate and NMDAR1 showed a significant reduction, whereas GABA, GABAB receptors, glycine receptors, and GluR2 exhibited a concomitant increase at P12. These features were present but less pronounced in hypoglossal nucleus and dorsal motor nucleus of the vagus and were absent in the cuneate nucleus. These data suggest that brain stem nuclei, directly or indirectly related to respiratory control, share a common developmental trend with the pre-Botzinger complex in having a transient period of imbalance between inhibitory and excitatory drives at P12. During this critical period, the respiratory system may be more vulnerable to excessive exogenous stressors.},
|
||||||
keywords = {Aging; Animals; Animals, Newborn; Brain Stem; Gene Expression Regulation, Developmental; Glutamic Acid; Neurotransmitter Agents; Rats; Rats, Sprague-Dawley; Receptors, AMPA; Receptors, GABA-B; Receptors, Glycine; Receptors, N-Methyl-D-Aspartate; Sensory Receptor Cells; Tissue Distribution; gamma-Aminobutyric Acid; },
|
keywords = {Aging; Animals; Animals, Newborn; Brain Stem; Gene Expression Regulation, Developmental; Glutamic Acid; Neurotransmitter Agents; Rats; Rats, Sprague-Dawley; Receptors, AMPA; Receptors, GABA-B; Receptors, Glycine; Receptors, N-Methyl-D-Aspartate; Sensory Receptor Cells; Tissue Distribution; gamma-Aminobutyric Acid; },
|
||||||
pubmed = {15618314},
|
pmid = {15618314},
|
||||||
pii = {01301.2004},
|
pii = {01301.2004},
|
||||||
doi = {10.1152/japplphysiol.01301.2004},
|
doi = {10.1152/japplphysiol.01301.2004},
|
||||||
url = {papers/Liu_JApplPhysiol(1985)2005-15618314.pdf},
|
url = {papers/Liu_JApplPhysiol(1985)2005-15618314.pdf},
|
||||||
@@ -113409,7 +113444,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {429-433},
|
pages = {429-433},
|
||||||
abstract = {Deep neural networks have achieved impressive successes in fields ranging from object recognition to complex games such as Go1,2. Navigation, however, remains a substantial challenge for artificial agents, with deep neural networks trained by reinforcement learning3-5 failing to rival the proficiency of mammalian spatial behaviour, which is underpinned by grid cells in the entorhinal cortex 6 . Grid cells are thought to provide a multi-scale periodic representation that functions as a metric for coding space7,8 and is critical for integrating self-motion (path integration)6,7,9 and planning direct trajectories to goals (vector-based navigation)7,10,11. Here we set out to leverage the computational functions of grid cells to develop a deep reinforcement learning agent with mammal-like navigational abilities. We first trained a recurrent network to perform path integration, leading to the emergence of representations resembling grid cells, as well as other entorhinal cell types 12 . We then showed that this representation provided an effective basis for an agent to locate goals in challenging, unfamiliar, and changeable environments-optimizing the primary objective of navigation through deep reinforcement learning. The performance of agents endowed with grid-like representations surpassed that of an expert human and comparison agents, with the metric quantities necessary for vector-based navigation derived from grid-like units within the network. Furthermore, grid-like representations enabled agents to conduct shortcut behaviours reminiscent of those performed by mammals. Our findings show that emergent grid-like representations furnish agents with a Euclidean spatial metric and associated vector operations, providing a foundation for proficient navigation. As such, our results support neuroscientific theories that see grid cells as critical for vector-based navigation7,10,11, demonstrating that the latter can be combined with path-based strategies to support navigation in challenging environments.},
|
abstract = {Deep neural networks have achieved impressive successes in fields ranging from object recognition to complex games such as Go1,2. Navigation, however, remains a substantial challenge for artificial agents, with deep neural networks trained by reinforcement learning3-5 failing to rival the proficiency of mammalian spatial behaviour, which is underpinned by grid cells in the entorhinal cortex 6 . Grid cells are thought to provide a multi-scale periodic representation that functions as a metric for coding space7,8 and is critical for integrating self-motion (path integration)6,7,9 and planning direct trajectories to goals (vector-based navigation)7,10,11. Here we set out to leverage the computational functions of grid cells to develop a deep reinforcement learning agent with mammal-like navigational abilities. We first trained a recurrent network to perform path integration, leading to the emergence of representations resembling grid cells, as well as other entorhinal cell types 12 . We then showed that this representation provided an effective basis for an agent to locate goals in challenging, unfamiliar, and changeable environments-optimizing the primary objective of navigation through deep reinforcement learning. The performance of agents endowed with grid-like representations surpassed that of an expert human and comparison agents, with the metric quantities necessary for vector-based navigation derived from grid-like units within the network. Furthermore, grid-like representations enabled agents to conduct shortcut behaviours reminiscent of those performed by mammals. Our findings show that emergent grid-like representations furnish agents with a Euclidean spatial metric and associated vector operations, providing a foundation for proficient navigation. As such, our results support neuroscientific theories that see grid cells as critical for vector-based navigation7,10,11, demonstrating that the latter can be combined with path-based strategies to support navigation in challenging environments.},
|
||||||
keywords = {Animals; Biomimetics; Entorhinal Cortex; Environment; Grid Cells; Humans; Machine Learning; Neural Networks, Computer; Spatial Navigation; },
|
keywords = {Animals; Biomimetics; Entorhinal Cortex; Environment; Grid Cells; Humans; Machine Learning; Neural Networks, Computer; Spatial Navigation; },
|
||||||
pubmed = {29743670},
|
pmid = {29743670},
|
||||||
doi = {10.1038/s41586-018-0102-6},
|
doi = {10.1038/s41586-018-0102-6},
|
||||||
pii = {10.1038/s41586-018-0102-6},
|
pii = {10.1038/s41586-018-0102-6},
|
||||||
url = {papers/Banino_Nature2018-29743670.pdf},
|
url = {papers/Banino_Nature2018-29743670.pdf},
|
||||||
@@ -113427,7 +113462,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {87-94},
|
pages = {87-94},
|
||||||
abstract = {Advanced imaging methods now allow cell-type-specific recording of neural activity across the mammalian brain, potentially enabling the exploration of how brain-wide dynamical patterns give rise to complex behavioural states1-12. Dissociation is an altered behavioural state in which the integrity of experience is disrupted, resulting in reproducible cognitive phenomena including the dissociation of stimulus detection from stimulus-related affective responses. Dissociation can occur as a result of trauma, epilepsy or dissociative drug use13,14, but despite its substantial basic and clinical importance, the underlying neurophysiology of this state is unknown. Here we establish such a dissociation-like state in mice, induced by precisely-dosed administration of ketamine or phencyclidine. Large-scale imaging of neural activity revealed that these dissociative agents elicited a 1-3-Hz rhythm in layer 5 neurons of the retrosplenial cortex. Electrophysiological recording with four simultaneously deployed high-density probes revealed rhythmic coupling of the retrosplenial cortex with anatomically connected components of thalamus circuitry, but uncoupling from most other brain regions was observed-including a notable inverse correlation with frontally projecting thalamic nuclei. In testing for causal significance, we found that rhythmic optogenetic activation of retrosplenial cortex layer 5 neurons recapitulated dissociation-like behavioural effects. Local retrosplenial hyperpolarization-activated cyclic-nucleotide-gated potassium channel 1 (HCN1) pacemakers were required for systemic ketamine to induce this rhythm and to elicit dissociation-like behavioural effects. In a patient with focal epilepsy, simultaneous intracranial stereoencephalography recordings from across the brain revealed a similarly localized rhythm in the homologous deep posteromedial cortex that was temporally correlated with pre-seizure self-reported dissociation, and local brief electrical stimulation of this region elicited dissociative experiences. These results identify the molecular, cellular and physiological properties of a conserved deep posteromedial cortical rhythm that underlies states of dissociation.},
|
abstract = {Advanced imaging methods now allow cell-type-specific recording of neural activity across the mammalian brain, potentially enabling the exploration of how brain-wide dynamical patterns give rise to complex behavioural states1-12. Dissociation is an altered behavioural state in which the integrity of experience is disrupted, resulting in reproducible cognitive phenomena including the dissociation of stimulus detection from stimulus-related affective responses. Dissociation can occur as a result of trauma, epilepsy or dissociative drug use13,14, but despite its substantial basic and clinical importance, the underlying neurophysiology of this state is unknown. Here we establish such a dissociation-like state in mice, induced by precisely-dosed administration of ketamine or phencyclidine. Large-scale imaging of neural activity revealed that these dissociative agents elicited a 1-3-Hz rhythm in layer 5 neurons of the retrosplenial cortex. Electrophysiological recording with four simultaneously deployed high-density probes revealed rhythmic coupling of the retrosplenial cortex with anatomically connected components of thalamus circuitry, but uncoupling from most other brain regions was observed-including a notable inverse correlation with frontally projecting thalamic nuclei. In testing for causal significance, we found that rhythmic optogenetic activation of retrosplenial cortex layer 5 neurons recapitulated dissociation-like behavioural effects. Local retrosplenial hyperpolarization-activated cyclic-nucleotide-gated potassium channel 1 (HCN1) pacemakers were required for systemic ketamine to induce this rhythm and to elicit dissociation-like behavioural effects. In a patient with focal epilepsy, simultaneous intracranial stereoencephalography recordings from across the brain revealed a similarly localized rhythm in the homologous deep posteromedial cortex that was temporally correlated with pre-seizure self-reported dissociation, and local brief electrical stimulation of this region elicited dissociative experiences. These results identify the molecular, cellular and physiological properties of a conserved deep posteromedial cortical rhythm that underlies states of dissociation.},
|
||||||
keywords = {Action Potentials; Animals; Behavior; Brain Waves; Cerebral Cortex; Dissociative Disorders; Electrophysiology; Female; Humans; Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels; Ketamine; Male; Mice; Mice, Inbred C57BL; Neurons; Optogenetics; Self Report; Thalamus; },
|
keywords = {Action Potentials; Animals; Behavior; Brain Waves; Cerebral Cortex; Dissociative Disorders; Electrophysiology; Female; Humans; Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels; Ketamine; Male; Mice; Mice, Inbred C57BL; Neurons; Optogenetics; Self Report; Thalamus; },
|
||||||
pubmed = {32939091},
|
pmid = {32939091},
|
||||||
doi = {10.1038/s41586-020-2731-9},
|
doi = {10.1038/s41586-020-2731-9},
|
||||||
pii = {10.1038/s41586-020-2731-9},
|
pii = {10.1038/s41586-020-2731-9},
|
||||||
pmc = {PMC7553818},
|
pmc = {PMC7553818},
|
||||||
@@ -113444,7 +113479,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
month = {Oct},
|
month = {Oct},
|
||||||
pages = {},
|
pages = {},
|
||||||
abstract = {Motor behavior results in complex exchanges of motor and sensory information across cortical regions. Therefore, fully understanding the cerebral cortex's role in motor behavior requires a mesoscopic-level description of the cortical regions engaged, their functional interactions, and how these functional interactions change with behavioral state. Mesoscopic Ca2+ imaging through transparent polymer skulls in mice reveals elevated activation of the dorsal cerebral cortex during locomotion. Using the correlations between the time series of Ca2+ fluorescence from 28 regions (nodes) obtained using spatial independent component analysis (sICA), we examined the changes in functional connectivity of the cortex from rest to locomotion with a goal of understanding the changes to the cortical functional state that facilitate locomotion. Both the transitions from rest to locomotion and from locomotion to rest show marked increases in correlation among most nodes. However, once a steady state of continued locomotion is reached, many nodes, including primary motor and somatosensory nodes, show decreases in correlations, while retrosplenial and the most anterior nodes of the secondary motor cortex show increases. These results highlight the changes in functional connectivity in the cerebral cortex, representing a series of changes in the cortical state from rest to locomotion and on return to rest.},
|
abstract = {Motor behavior results in complex exchanges of motor and sensory information across cortical regions. Therefore, fully understanding the cerebral cortex's role in motor behavior requires a mesoscopic-level description of the cortical regions engaged, their functional interactions, and how these functional interactions change with behavioral state. Mesoscopic Ca2+ imaging through transparent polymer skulls in mice reveals elevated activation of the dorsal cerebral cortex during locomotion. Using the correlations between the time series of Ca2+ fluorescence from 28 regions (nodes) obtained using spatial independent component analysis (sICA), we examined the changes in functional connectivity of the cortex from rest to locomotion with a goal of understanding the changes to the cortical functional state that facilitate locomotion. Both the transitions from rest to locomotion and from locomotion to rest show marked increases in correlation among most nodes. However, once a steady state of continued locomotion is reached, many nodes, including primary motor and somatosensory nodes, show decreases in correlations, while retrosplenial and the most anterior nodes of the secondary motor cortex show increases. These results highlight the changes in functional connectivity in the cerebral cortex, representing a series of changes in the cortical state from rest to locomotion and on return to rest.},
|
||||||
pubmed = {34689209},
|
pmid = {34689209},
|
||||||
pii = {6408797},
|
pii = {6408797},
|
||||||
doi = {10.1093/cercor/bhab373},
|
doi = {10.1093/cercor/bhab373},
|
||||||
url = {papers/West_CerebCortex2022-34689209.pdf},
|
url = {papers/West_CerebCortex2022-34689209.pdf},
|
||||||
@@ -113461,7 +113496,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {},
|
pages = {},
|
||||||
abstract = {Widefield fluorescence microscopy is used to monitor the spiking of populations of neurons in the brain. Widefield fluorescence can originate from indicator molecules at all depths in cortex and the relative contributions from somata, dendrites, and axons are often unknown. Here, I simulate widefield illumination and fluorescence collection and determine the main sources of fluorescence for several GCaMP mouse lines. Scattering strongly affects illumination and collection. One consequence is that illumination intensity is greatest ~300-400 µm below the pia, not at the brain surface. Another is that fluorescence from a source deep in cortex may extend across a diameter of 3-4 mm at the brain surface, severely limiting lateral resolution. In many mouse lines, the volume of tissue contributing to fluorescence extends through the full depth of cortex and fluorescence at most surface locations is a weighted average across multiple cortical columns and often more than one cortical area.},
|
abstract = {Widefield fluorescence microscopy is used to monitor the spiking of populations of neurons in the brain. Widefield fluorescence can originate from indicator molecules at all depths in cortex and the relative contributions from somata, dendrites, and axons are often unknown. Here, I simulate widefield illumination and fluorescence collection and determine the main sources of fluorescence for several GCaMP mouse lines. Scattering strongly affects illumination and collection. One consequence is that illumination intensity is greatest ~300-400 µm below the pia, not at the brain surface. Another is that fluorescence from a source deep in cortex may extend across a diameter of 3-4 mm at the brain surface, severely limiting lateral resolution. In many mouse lines, the volume of tissue contributing to fluorescence extends through the full depth of cortex and fluorescence at most surface locations is a weighted average across multiple cortical columns and often more than one cortical area.},
|
||||||
keywords = {cortex; fluorescence; imaging; microscopy; neuroscience; none; widefield; Animals; Brain; Cell Line; Fluorescence; Mice; Microscopy, Fluorescence; Monte Carlo Method; },
|
keywords = {cortex; fluorescence; imaging; microscopy; neuroscience; none; widefield; Animals; Brain; Cell Line; Fluorescence; Mice; Microscopy, Fluorescence; Monte Carlo Method; },
|
||||||
pubmed = {33155981},
|
pmid = {33155981},
|
||||||
doi = {10.7554/eLife.59841},
|
doi = {10.7554/eLife.59841},
|
||||||
pii = {59841},
|
pii = {59841},
|
||||||
pmc = {PMC7647397},
|
pmc = {PMC7647397},
|
||||||
@@ -113477,7 +113512,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
number = {3},
|
number = {3},
|
||||||
pages = {160-188},
|
pages = {160-188},
|
||||||
keywords = {functional magnetic resonance imaging, independent component analysis, higher-order statistics},
|
keywords = {functional magnetic resonance imaging, independent component analysis, higher-order statistics},
|
||||||
pubmed = {9673671},
|
pmid = {9673671},
|
||||||
doi = {10.1002/(SICI)1097-0193(1998)6:3<160::AID-HBM5>3.0.CO;2-1},
|
doi = {10.1002/(SICI)1097-0193(1998)6:3<160::AID-HBM5>3.0.CO;2-1},
|
||||||
url = {Mckeown_HumBrainMap1998.pdf},
|
url = {Mckeown_HumBrainMap1998.pdf},
|
||||||
abstract = {Abstract Current analytical techniques applied to functional magnetic resonance imaging (fMRI) data require a priori knowledge or specific assumptions about the time courses of processes contributing to the measured signals. Here we describe a new method for analyzing fMRI data based on the independent component analysis (ICA) algorithm of Bell and Sejnowski ([1995]: Neural Comput 7:1129–1159). We decomposed eight fMRI data sets from 4 normal subjects performing Stroop color-naming, the Brown and Peterson word/number task, and control tasks into spatially independent components. Each component consisted of voxel values at fixed three-dimensional locations (a component “map”), and a unique associated time course of activation. Given data from 144 time points collected during a 6-min trial, ICA extracted an equal number of spatially independent components. In all eight trials, ICA derived one and only one component with a time course closely matching the time course of 40-sec alternations between experimental and control tasks. The regions of maximum activity in these consistently task-related components generally overlapped active regions detected by standard correlational analysis, but included frontal regions not detected by correlation. Time courses of other ICA components were transiently task-related, quasiperiodic, or slowly varying. By utilizing higher-order statistics to enforce successively stricter criteria for spatial independence between component maps, both the ICA algorithm and a related fourth-order decomposition technique (Comon [1994]: Signal Processing 36:11–20) were superior to principal component analysis (PCA) in determining the spatial and temporal extent of task-related activation. For each subject, the time courses and active regions of the task-related ICA components were consistent across trials and were robust to the addition of simulated noise. Simulated movement artifact and simulated task-related activations added to actual fMRI data were clearly separated by the algorithm. ICA can be used to distinguish between nontask-related signal components, movements, and other artifacts, as well as consistently or transiently task-related fMRI activations, based on only weak assumptions about their spatial distributions and without a priori assumptions about their time courses. ICA appears to be a highly promising method for the analysis of fMRI data from normal and clinical populations, especially for uncovering unpredictable transient patterns of brain activity associated with performance of psychomotor tasks. Hum. Brain Mapping 6:160–188, 1998. © 1998 Wiley-Liss, Inc.},
|
abstract = {Abstract Current analytical techniques applied to functional magnetic resonance imaging (fMRI) data require a priori knowledge or specific assumptions about the time courses of processes contributing to the measured signals. Here we describe a new method for analyzing fMRI data based on the independent component analysis (ICA) algorithm of Bell and Sejnowski ([1995]: Neural Comput 7:1129–1159). We decomposed eight fMRI data sets from 4 normal subjects performing Stroop color-naming, the Brown and Peterson word/number task, and control tasks into spatially independent components. Each component consisted of voxel values at fixed three-dimensional locations (a component “map”), and a unique associated time course of activation. Given data from 144 time points collected during a 6-min trial, ICA extracted an equal number of spatially independent components. In all eight trials, ICA derived one and only one component with a time course closely matching the time course of 40-sec alternations between experimental and control tasks. The regions of maximum activity in these consistently task-related components generally overlapped active regions detected by standard correlational analysis, but included frontal regions not detected by correlation. Time courses of other ICA components were transiently task-related, quasiperiodic, or slowly varying. By utilizing higher-order statistics to enforce successively stricter criteria for spatial independence between component maps, both the ICA algorithm and a related fourth-order decomposition technique (Comon [1994]: Signal Processing 36:11–20) were superior to principal component analysis (PCA) in determining the spatial and temporal extent of task-related activation. For each subject, the time courses and active regions of the task-related ICA components were consistent across trials and were robust to the addition of simulated noise. Simulated movement artifact and simulated task-related activations added to actual fMRI data were clearly separated by the algorithm. ICA can be used to distinguish between nontask-related signal components, movements, and other artifacts, as well as consistently or transiently task-related fMRI activations, based on only weak assumptions about their spatial distributions and without a priori assumptions about their time courses. ICA appears to be a highly promising method for the analysis of fMRI data from normal and clinical populations, especially for uncovering unpredictable transient patterns of brain activity associated with performance of psychomotor tasks. Hum. Brain Mapping 6:160–188, 1998. © 1998 Wiley-Liss, Inc.},
|
||||||
@@ -113494,7 +113529,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {267-277},
|
pages = {267-277},
|
||||||
abstract = {Head motion during functional MRI (fMRI) scanning can induce spurious findings and/or harm detection of true effects. Solutions have been proposed, including deleting ('scrubbing') or regressing out ('spike regression') motion volumes from fMRI time-series. These strategies remove motion-induced signal variations at the cost of destroying the autocorrelation structure of the fMRI time-series and reducing temporal degrees of freedom. ICA-based fMRI denoising strategies overcome these drawbacks but typically require re-training of a classifier, needing manual labeling of derived components (e.g. ICA-FIX; Salimi-Khorshidi et al. (2014)). Here, we propose an ICA-based strategy for Automatic Removal of Motion Artifacts (ICA-AROMA) that uses a small (n=4), but robust set of theoretically motivated temporal and spatial features. Our strategy does not require classifier re-training, retains the data's autocorrelation structure and largely preserves temporal degrees of freedom. We describe ICA-AROMA, its implementation, and initial validation. ICA-AROMA identified motion components with high accuracy and robustness as illustrated by leave-N-out cross-validation. We additionally validated ICA-AROMA in resting-state (100 participants) and task-based fMRI data (118 participants). Our approach removed (motion-related) spurious noise from both rfMRI and task-based fMRI data to larger extent than regression using 24 motion parameters or spike regression. Furthermore, ICA-AROMA increased sensitivity to group-level activation. Our results show that ICA-AROMA effectively reduces motion-induced signal variations in fMRI data, is applicable across datasets without requiring classifier re-training, and preserves the temporal characteristics of the fMRI data. },
|
abstract = {Head motion during functional MRI (fMRI) scanning can induce spurious findings and/or harm detection of true effects. Solutions have been proposed, including deleting ('scrubbing') or regressing out ('spike regression') motion volumes from fMRI time-series. These strategies remove motion-induced signal variations at the cost of destroying the autocorrelation structure of the fMRI time-series and reducing temporal degrees of freedom. ICA-based fMRI denoising strategies overcome these drawbacks but typically require re-training of a classifier, needing manual labeling of derived components (e.g. ICA-FIX; Salimi-Khorshidi et al. (2014)). Here, we propose an ICA-based strategy for Automatic Removal of Motion Artifacts (ICA-AROMA) that uses a small (n=4), but robust set of theoretically motivated temporal and spatial features. Our strategy does not require classifier re-training, retains the data's autocorrelation structure and largely preserves temporal degrees of freedom. We describe ICA-AROMA, its implementation, and initial validation. ICA-AROMA identified motion components with high accuracy and robustness as illustrated by leave-N-out cross-validation. We additionally validated ICA-AROMA in resting-state (100 participants) and task-based fMRI data (118 participants). Our approach removed (motion-related) spurious noise from both rfMRI and task-based fMRI data to larger extent than regression using 24 motion parameters or spike regression. Furthermore, ICA-AROMA increased sensitivity to group-level activation. Our results show that ICA-AROMA effectively reduces motion-induced signal variations in fMRI data, is applicable across datasets without requiring classifier re-training, and preserves the temporal characteristics of the fMRI data. },
|
||||||
keywords = {Artifact; Connectivity; Functional MRI; Independent component analysis; Motion; Resting state; Algorithms; Artifacts; Artificial Intelligence; Cerebrospinal Fluid; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Motion; Principal Component Analysis; Reproducibility of Results; Rest; },
|
keywords = {Artifact; Connectivity; Functional MRI; Independent component analysis; Motion; Resting state; Algorithms; Artifacts; Artificial Intelligence; Cerebrospinal Fluid; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Motion; Principal Component Analysis; Reproducibility of Results; Rest; },
|
||||||
pubmed = {25770991},
|
pmid = {25770991},
|
||||||
pii = {S1053-8119(15)00182-2},
|
pii = {S1053-8119(15)00182-2},
|
||||||
doi = {10.1016/j.neuroimage.2015.02.064},
|
doi = {10.1016/j.neuroimage.2015.02.064},
|
||||||
url = {papers/Pruim_Neuroimage2016-25770991.pdf},
|
url = {papers/Pruim_Neuroimage2016-25770991.pdf},
|
||||||
@@ -113511,7 +113546,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {415-436},
|
pages = {415-436},
|
||||||
abstract = {Estimates of functional connectivity derived from resting-state functional magnetic resonance imaging (rs-fMRI) are sensitive to artefacts caused by in-scanner head motion. This susceptibility has motivated the development of numerous denoising methods designed to mitigate motion-related artefacts. Here, we compare popular retrospective rs-fMRI denoising methods, such as regression of head motion parameters and mean white matter (WM) and cerebrospinal fluid (CSF) (with and without expansion terms), aCompCor, volume censoring (e.g., scrubbing and spike regression), global signal regression and ICA-AROMA, combined into 19 different pipelines. These pipelines were evaluated across five different quality control benchmarks in four independent datasets associated with varying levels of motion. Pipelines were benchmarked by examining the residual relationship between in-scanner movement and functional connectivity after denoising; the effect of distance on this residual relationship; whole-brain differences in functional connectivity between high- and low-motion healthy controls (HC); the temporal degrees of freedom lost during denoising; and the test-retest reliability of functional connectivity estimates. We also compared the sensitivity of each pipeline to clinical differences in functional connectivity in independent samples of people with schizophrenia and obsessive-compulsive disorder. Our results indicate that (1) simple linear regression of regional fMRI time series against head motion parameters and WM/CSF signals (with or without expansion terms) is not sufficient to remove head motion artefacts; (2) aCompCor pipelines may only be viable in low-motion data; (3) volume censoring performs well at minimising motion-related artefact but a major benefit of this approach derives from the exclusion of high-motion individuals; (4) while not as effective as volume censoring, ICA-AROMA performed well across our benchmarks for relatively low cost in terms of data loss; (5) the addition of global signal regression improved the performance of nearly all pipelines on most benchmarks, but exacerbated the distance-dependence of correlations between motion and functional connectivity; and (6) group comparisons in functional connectivity between healthy controls and schizophrenia patients are highly dependent on preprocessing strategy. We offer some recommendations for best practice and outline simple analyses to facilitate transparent reporting of the degree to which a given set of findings may be affected by motion-related artefact.},
|
abstract = {Estimates of functional connectivity derived from resting-state functional magnetic resonance imaging (rs-fMRI) are sensitive to artefacts caused by in-scanner head motion. This susceptibility has motivated the development of numerous denoising methods designed to mitigate motion-related artefacts. Here, we compare popular retrospective rs-fMRI denoising methods, such as regression of head motion parameters and mean white matter (WM) and cerebrospinal fluid (CSF) (with and without expansion terms), aCompCor, volume censoring (e.g., scrubbing and spike regression), global signal regression and ICA-AROMA, combined into 19 different pipelines. These pipelines were evaluated across five different quality control benchmarks in four independent datasets associated with varying levels of motion. Pipelines were benchmarked by examining the residual relationship between in-scanner movement and functional connectivity after denoising; the effect of distance on this residual relationship; whole-brain differences in functional connectivity between high- and low-motion healthy controls (HC); the temporal degrees of freedom lost during denoising; and the test-retest reliability of functional connectivity estimates. We also compared the sensitivity of each pipeline to clinical differences in functional connectivity in independent samples of people with schizophrenia and obsessive-compulsive disorder. Our results indicate that (1) simple linear regression of regional fMRI time series against head motion parameters and WM/CSF signals (with or without expansion terms) is not sufficient to remove head motion artefacts; (2) aCompCor pipelines may only be viable in low-motion data; (3) volume censoring performs well at minimising motion-related artefact but a major benefit of this approach derives from the exclusion of high-motion individuals; (4) while not as effective as volume censoring, ICA-AROMA performed well across our benchmarks for relatively low cost in terms of data loss; (5) the addition of global signal regression improved the performance of nearly all pipelines on most benchmarks, but exacerbated the distance-dependence of correlations between motion and functional connectivity; and (6) group comparisons in functional connectivity between healthy controls and schizophrenia patients are highly dependent on preprocessing strategy. We offer some recommendations for best practice and outline simple analyses to facilitate transparent reporting of the degree to which a given set of findings may be affected by motion-related artefact.},
|
||||||
keywords = {Artefact; Functional connectivity; Motion; Noise; Resting-state; fMRI; Adult; Algorithms; Artifacts; Brain Mapping; Datasets as Topic; Female; Head Movements; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Motion; Reproducibility of Results; },
|
keywords = {Artefact; Functional connectivity; Motion; Noise; Resting-state; fMRI; Adult; Algorithms; Artifacts; Brain Mapping; Datasets as Topic; Female; Head Movements; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Motion; Reproducibility of Results; },
|
||||||
pubmed = {29278773},
|
pmid = {29278773},
|
||||||
pii = {S1053-8119(17)31097-2},
|
pii = {S1053-8119(17)31097-2},
|
||||||
doi = {10.1016/j.neuroimage.2017.12.073},
|
doi = {10.1016/j.neuroimage.2017.12.073},
|
||||||
url = {papers/Parkes_Neuroimage2018-29278773.pdf},
|
url = {papers/Parkes_Neuroimage2018-29278773.pdf},
|
||||||
@@ -113528,7 +113563,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {11611},
|
pages = {11611},
|
||||||
abstract = {Mouse head-fixed behaviour coupled with functional imaging has become a powerful technique in rodent systems neuroscience. However, training mice can be time consuming and is potentially stressful for animals. Here we report a fully automated, open source, self-initiated head-fixation system for mesoscopic functional imaging in mice. The system supports five mice at a time and requires minimal investigator intervention. Using genetically encoded calcium indicator transgenic mice, we longitudinally monitor cortical functional connectivity up to 24 h per day in >7,000 self-initiated and unsupervised imaging sessions up to 90 days. The procedure provides robust assessment of functional cortical maps on the basis of both spontaneous activity and brief sensory stimuli such as light flashes. The approach is scalable to a number of remotely controlled cages that can be assessed within the controlled conditions of dedicated animal facilities. We anticipate that home-cage brain imaging will permit flexible and chronic assessment of mesoscale cortical function.},
|
abstract = {Mouse head-fixed behaviour coupled with functional imaging has become a powerful technique in rodent systems neuroscience. However, training mice can be time consuming and is potentially stressful for animals. Here we report a fully automated, open source, self-initiated head-fixation system for mesoscopic functional imaging in mice. The system supports five mice at a time and requires minimal investigator intervention. Using genetically encoded calcium indicator transgenic mice, we longitudinally monitor cortical functional connectivity up to 24 h per day in >7,000 self-initiated and unsupervised imaging sessions up to 90 days. The procedure provides robust assessment of functional cortical maps on the basis of both spontaneous activity and brief sensory stimuli such as light flashes. The approach is scalable to a number of remotely controlled cages that can be assessed within the controlled conditions of dedicated animal facilities. We anticipate that home-cage brain imaging will permit flexible and chronic assessment of mesoscale cortical function.},
|
||||||
keywords = {Animals; Automation; Evoked Potentials, Visual; Female; Head; Imaging, Three-Dimensional; Mice; Mice, Transgenic; Nerve Net; Visual Cortex; },
|
keywords = {Animals; Automation; Evoked Potentials, Visual; Female; Head; Imaging, Three-Dimensional; Mice; Mice, Transgenic; Nerve Net; Visual Cortex; },
|
||||||
pubmed = {27291514},
|
pmid = {27291514},
|
||||||
pii = {ncomms11611},
|
pii = {ncomms11611},
|
||||||
doi = {10.1038/ncomms11611},
|
doi = {10.1038/ncomms11611},
|
||||||
pmc = {PMC4909937},
|
pmc = {PMC4909937},
|
||||||
@@ -113547,7 +113582,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {137-52},
|
pages = {137-52},
|
||||||
abstract = {We present an integrated approach to probabilistic independent component analysis (ICA) for functional MRI (FMRI) data that allows for nonsquare mixing in the presence of Gaussian noise. In order to avoid overfitting, we employ objective estimation of the amount of Gaussian noise through Bayesian analysis of the true dimensionality of the data, i.e., the number of activation and non-Gaussian noise sources. This enables us to carry out probabilistic modeling and achieves an asymptotically unique decomposition of the data. It reduces problems of interpretation, as each final independent component is now much more likely to be due to only one physical or physiological process. We also describe other improvements to standard ICA, such as temporal prewhitening and variance normalization of timeseries, the latter being particularly useful in the context of dimensionality reduction when weak activation is present. We discuss the use of prior information about the spatiotemporal nature of the source processes, and an alternative-hypothesis testing approach for inference, using Gaussian mixture models. The performance of our approach is illustrated and evaluated on real and artificial FMRI data, and compared to the spatio-temporal accuracy of results obtained from classical ICA and GLM analyses.},
|
abstract = {We present an integrated approach to probabilistic independent component analysis (ICA) for functional MRI (FMRI) data that allows for nonsquare mixing in the presence of Gaussian noise. In order to avoid overfitting, we employ objective estimation of the amount of Gaussian noise through Bayesian analysis of the true dimensionality of the data, i.e., the number of activation and non-Gaussian noise sources. This enables us to carry out probabilistic modeling and achieves an asymptotically unique decomposition of the data. It reduces problems of interpretation, as each final independent component is now much more likely to be due to only one physical or physiological process. We also describe other improvements to standard ICA, such as temporal prewhitening and variance normalization of timeseries, the latter being particularly useful in the context of dimensionality reduction when weak activation is present. We discuss the use of prior information about the spatiotemporal nature of the source processes, and an alternative-hypothesis testing approach for inference, using Gaussian mixture models. The performance of our approach is illustrated and evaluated on real and artificial FMRI data, and compared to the spatio-temporal accuracy of results obtained from classical ICA and GLM analyses.},
|
||||||
keywords = {Algorithms; Brain; Cerebral Cortex; Humans; Image Enhancement; Image Interpretation, Computer-Assisted; Magnetic Resonance Imaging; Models, Neurological; Models, Statistical; Neurons; Phantoms, Imaging; Principal Component Analysis; Reproducibility of Results; Sensitivity and Specificity; Stochastic Processes; Vision, Ocular; },
|
keywords = {Algorithms; Brain; Cerebral Cortex; Humans; Image Enhancement; Image Interpretation, Computer-Assisted; Magnetic Resonance Imaging; Models, Neurological; Models, Statistical; Neurons; Phantoms, Imaging; Principal Component Analysis; Reproducibility of Results; Sensitivity and Specificity; Stochastic Processes; Vision, Ocular; },
|
||||||
pubmed = {14964560},
|
pmid = {14964560},
|
||||||
doi = {10.1109/TMI.2003.822821},
|
doi = {10.1109/TMI.2003.822821},
|
||||||
url = {papers/Beckmann_IEEETransMedImaging2004-14964560.pdf},
|
url = {papers/Beckmann_IEEETransMedImaging2004-14964560.pdf},
|
||||||
nlmuniqueid = {8310780}
|
nlmuniqueid = {8310780}
|
||||||
@@ -113564,7 +113599,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {778-786},
|
pages = {778-786},
|
||||||
abstract = {The interactions between neocortical areas are fluid and state-dependent, but how individual neurons couple to cortex-wide network dynamics remains poorly understood. We correlated the spiking of neurons in primary visual (V1) and retrosplenial (RSP) cortex to activity across dorsal cortex, recorded simultaneously by widefield calcium imaging. Neurons were correlated with distinct and reproducible patterns of activity across the cortical surface; while some fired predominantly with their local area, others coupled to activity in distal areas. The extent of distal coupling was predicted by how strongly neurons correlated with the local network. Changes in brain state triggered by locomotion strengthened affiliations of V1 neurons with higher visual and motor areas, while strengthening distal affiliations of RSP neurons with sensory cortices. Thus, the diverse coupling of individual neurons to cortex-wide activity patterns is restructured by running in an area-specific manner, resulting in a shift in the mode of cortical processing during locomotion.},
|
abstract = {The interactions between neocortical areas are fluid and state-dependent, but how individual neurons couple to cortex-wide network dynamics remains poorly understood. We correlated the spiking of neurons in primary visual (V1) and retrosplenial (RSP) cortex to activity across dorsal cortex, recorded simultaneously by widefield calcium imaging. Neurons were correlated with distinct and reproducible patterns of activity across the cortical surface; while some fired predominantly with their local area, others coupled to activity in distal areas. The extent of distal coupling was predicted by how strongly neurons correlated with the local network. Changes in brain state triggered by locomotion strengthened affiliations of V1 neurons with higher visual and motor areas, while strengthening distal affiliations of RSP neurons with sensory cortices. Thus, the diverse coupling of individual neurons to cortex-wide activity patterns is restructured by running in an area-specific manner, resulting in a shift in the mode of cortical processing during locomotion.},
|
||||||
keywords = {Action Potentials; Animals; Cerebral Cortex; Female; Locomotion; Male; Mice, Transgenic; Neural Pathways; Neurons; Visual Cortex; },
|
keywords = {Action Potentials; Animals; Cerebral Cortex; Female; Locomotion; Male; Mice, Transgenic; Neural Pathways; Neurons; Visual Cortex; },
|
||||||
pubmed = {30858604},
|
pmid = {30858604},
|
||||||
doi = {10.1038/s41593-019-0357-8},
|
doi = {10.1038/s41593-019-0357-8},
|
||||||
pii = {10.1038/s41593-019-0357-8},
|
pii = {10.1038/s41593-019-0357-8},
|
||||||
pmc = {PMC6701985},
|
pmc = {PMC6701985},
|
||||||
@@ -113584,7 +113619,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {7513-7533},
|
pages = {7513-7533},
|
||||||
abstract = {Connectivity mapping based on resting-state activity in mice has revealed functional motifs of correlated activity. However, the rules by which motifs organize into larger functional modules that lead to hemisphere wide spatial-temporal activity sequences is not clear. We explore cortical activity parcellation in head-fixed, quiet awake GCaMP6 mice from both sexes by using mesoscopic calcium imaging. Spectral decomposition of spontaneous cortical activity revealed the presence of two dominant frequency modes (<1 and ∼3 Hz), each of them associated with a unique spatial signature of cortical macro-parcellation not predicted by classical cytoarchitectonic definitions of cortical areas. Based on assessment of 0.1-1 Hz activity, we define two macro-organizing principles: the first being a rotating polymodal-association pinwheel structure around which activity flows sequentially from visual to barrel then to hindlimb somatosensory; the second principle is correlated activity symmetry planes that exist on many levels within a single domain such as intrahemispheric reflections of sensory and motor cortices. In contrast, higher frequency activity >1 Hz yielded two larger clusters of coactivated areas with an enlarged default mode network-like posterior region. We suggest that the apparent constrained structure for intra-areal cortical activity flow could be exploited in future efforts to normalize activity in diseases of the nervous system.SIGNIFICANCE STATEMENT Increasingly, functional connectivity mapping of spontaneous activity is being used to reveal the organization of the brain. However, because the brain operates across multiple space and time domains a more detailed understanding of this organization is necessary. We used in vivo wide-field calcium imaging of the indicator GCaMP6 in head-fixed, awake mice to characterize the organization of spontaneous cortical activity at different spatiotemporal scales. Correlation analysis defines the presence of two to three superclusters of activity that span traditionally defined functional territories and were frequency dependent. This work helps define the rules for how different cortical areas interact in time and space. We provide a framework necessary for future studies that explore functional reorganization of brain circuits in disease models.},
|
abstract = {Connectivity mapping based on resting-state activity in mice has revealed functional motifs of correlated activity. However, the rules by which motifs organize into larger functional modules that lead to hemisphere wide spatial-temporal activity sequences is not clear. We explore cortical activity parcellation in head-fixed, quiet awake GCaMP6 mice from both sexes by using mesoscopic calcium imaging. Spectral decomposition of spontaneous cortical activity revealed the presence of two dominant frequency modes (<1 and ∼3 Hz), each of them associated with a unique spatial signature of cortical macro-parcellation not predicted by classical cytoarchitectonic definitions of cortical areas. Based on assessment of 0.1-1 Hz activity, we define two macro-organizing principles: the first being a rotating polymodal-association pinwheel structure around which activity flows sequentially from visual to barrel then to hindlimb somatosensory; the second principle is correlated activity symmetry planes that exist on many levels within a single domain such as intrahemispheric reflections of sensory and motor cortices. In contrast, higher frequency activity >1 Hz yielded two larger clusters of coactivated areas with an enlarged default mode network-like posterior region. We suggest that the apparent constrained structure for intra-areal cortical activity flow could be exploited in future efforts to normalize activity in diseases of the nervous system.SIGNIFICANCE STATEMENT Increasingly, functional connectivity mapping of spontaneous activity is being used to reveal the organization of the brain. However, because the brain operates across multiple space and time domains a more detailed understanding of this organization is necessary. We used in vivo wide-field calcium imaging of the indicator GCaMP6 in head-fixed, awake mice to characterize the organization of spontaneous cortical activity at different spatiotemporal scales. Correlation analysis defines the presence of two to three superclusters of activity that span traditionally defined functional territories and were frequency dependent. This work helps define the rules for how different cortical areas interact in time and space. We provide a framework necessary for future studies that explore functional reorganization of brain circuits in disease models.},
|
||||||
keywords = {awake mouse; calcium imaging; connectome; cortical dynamic; resting state; Animals; Brain Waves; Calcium Signaling; Cerebral Cortex; Computer Simulation; Connectome; Female; Male; Mice; Mice, Transgenic; Models, Neurological; Nerve Net; Rest; Spatio-Temporal Analysis; Voltage-Sensitive Dye Imaging; },
|
keywords = {awake mouse; calcium imaging; connectome; cortical dynamic; resting state; Animals; Brain Waves; Calcium Signaling; Cerebral Cortex; Computer Simulation; Connectome; Female; Male; Mice; Mice, Transgenic; Models, Neurological; Nerve Net; Rest; Spatio-Temporal Analysis; Voltage-Sensitive Dye Imaging; },
|
||||||
pubmed = {28674167},
|
pmid = {28674167},
|
||||||
pii = {JNEUROSCI.3560-16.2017},
|
pii = {JNEUROSCI.3560-16.2017},
|
||||||
doi = {10.1523/JNEUROSCI.3560-16.2017},
|
doi = {10.1523/JNEUROSCI.3560-16.2017},
|
||||||
pmc = {PMC6596702},
|
pmc = {PMC6596702},
|
||||||
@@ -113603,7 +113638,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
pages = {891-907.e6},
|
pages = {891-907.e6},
|
||||||
abstract = {The successful planning and execution of adaptive behaviors in mammals may require long-range coordination of neural networks throughout cerebral cortex. The neuronal implementation of signals that could orchestrate cortex-wide activity remains unclear. Here, we develop and apply methods for cortex-wide Ca2+ imaging in mice performing decision-making behavior and identify a global cortical representation of task engagement encoded in the activity dynamics of both single cells and superficial neuropil distributed across the majority of dorsal cortex. The activity of multiple molecularly defined cell types was found to reflect this representation with type-specific dynamics. Focal optogenetic inhibition tiled across cortex revealed a crucial role for frontal cortex in triggering this cortex-wide phenomenon; local inhibition of this region blocked both the cortex-wide response to task-initiating cues and the voluntary behavior. These findings reveal cell-type-specific processes in cortex for globally representing goal-directed behavior and identify a major cortical node that gates the global broadcast of task-related information.},
|
abstract = {The successful planning and execution of adaptive behaviors in mammals may require long-range coordination of neural networks throughout cerebral cortex. The neuronal implementation of signals that could orchestrate cortex-wide activity remains unclear. Here, we develop and apply methods for cortex-wide Ca2+ imaging in mice performing decision-making behavior and identify a global cortical representation of task engagement encoded in the activity dynamics of both single cells and superficial neuropil distributed across the majority of dorsal cortex. The activity of multiple molecularly defined cell types was found to reflect this representation with type-specific dynamics. Focal optogenetic inhibition tiled across cortex revealed a crucial role for frontal cortex in triggering this cortex-wide phenomenon; local inhibition of this region blocked both the cortex-wide response to task-initiating cues and the voluntary behavior. These findings reveal cell-type-specific processes in cortex for globally representing goal-directed behavior and identify a major cortical node that gates the global broadcast of task-related information.},
|
||||||
keywords = {calcium imaging; cell type; cortex; goal-directed behavior; optogenetics; widefield; Animals; Behavior, Animal; Calcium; Decision Making; Frontal Lobe; Goals; Mice; Neocortex; Neurons; Optical Imaging; Optogenetics; },
|
keywords = {calcium imaging; cell type; cortex; goal-directed behavior; optogenetics; widefield; Animals; Behavior, Animal; Calcium; Decision Making; Frontal Lobe; Goals; Mice; Neocortex; Neurons; Optical Imaging; Optogenetics; },
|
||||||
pubmed = {28521139},
|
pmid = {28521139},
|
||||||
pii = {S0896-6273(17)30343-4},
|
pii = {S0896-6273(17)30343-4},
|
||||||
doi = {10.1016/j.neuron.2017.04.017},
|
doi = {10.1016/j.neuron.2017.04.017},
|
||||||
pmc = {PMC5723385},
|
pmc = {PMC5723385},
|
||||||
@@ -113612,3 +113647,140 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
|
|||||||
nlmuniqueid = {8809320}
|
nlmuniqueid = {8809320}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@article{Esposito2005,
|
||||||
|
title = {Independent component analysis of fMRI group studies by self-organizing clustering.},
|
||||||
|
author = {Esposito, Fabrizio and Scarabino, Tommaso and Hyvarinen, Aapo and Himberg, Johan and Formisano, Elia and Comani, Silvia and Tedeschi, Gioacchino and Goebel, Rainer and Seifritz, Erich and Di Salle, Francesco},
|
||||||
|
journal = {Neuroimage},
|
||||||
|
volume = {25},
|
||||||
|
number = {1},
|
||||||
|
year = {2005},
|
||||||
|
month = {Mar},
|
||||||
|
pages = {193-205},
|
||||||
|
abstract = {Independent component analysis (ICA) is a valuable technique for the multivariate data-driven analysis of functional magnetic resonance imaging (fMRI) data sets. Applications of ICA have been developed mainly for single subject studies, although different solutions for group studies have been proposed. These approaches combine data sets from multiple subjects into a single aggregate data set before ICA estimation and, thus, require some additional assumptions about the separability across subjects of group independent components. Here, we exploit the application of similarity measures and a related visual tool to study the natural self-organizing clustering of many independent components from multiple individual data sets in the subject space. Our proposed framework flexibly enables multiple criteria for the generation of group independent components and their random-effects evaluation. We present real visual activation fMRI data from two experiments, with different spatiotemporal structures, and demonstrate the validity of this framework for a blind extraction and selection of meaningful activity and functional connectivity group patterns. Our approach is either alternative or complementary to the group ICA of aggregated data sets in that it exploits commonalities across multiple subject-specific patterns, while addressing as much as possible of the intersubject variability of the measured responses. This property is particularly of interest for a blind group and subgroup pattern extraction and selection.},
|
||||||
|
keywords = {Adult; Brain Mapping; Cluster Analysis; Dominance, Cerebral; Female; Humans; Image Processing, Computer-Assisted; Imaging, Three-Dimensional; Magnetic Resonance Imaging; Male; Numerical Analysis, Computer-Assisted; Pattern Recognition, Visual; Photic Stimulation; Principal Component Analysis; Reference Values; Reproducibility of Results; Visual Cortex; },
|
||||||
|
pmid = {15734355},
|
||||||
|
pii = {S1053-8119(04)00660-3},
|
||||||
|
doi = {10.1016/j.neuroimage.2004.10.042},
|
||||||
|
url = {papers/Esposito_Neuroimage2005-15734355.pdf},
|
||||||
|
nlmuniqueid = {9215515}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{Wei2017,
|
||||||
|
title = {Postnatal Craniofacial Skeletal Development of Female C57BL/6NCrl Mice.},
|
||||||
|
author = {Wei, Xiaoxi and Thomas, Neil and Hatch, Nan E and Hu, Min and Liu, Fei},
|
||||||
|
journal = {Front Physiol},
|
||||||
|
volume = {8},
|
||||||
|
year = {2017},
|
||||||
|
pages = {697},
|
||||||
|
abstract = {The craniofacial skeleton is a complex and unique structure. The perturbation of its development can lead to craniofacial dysmorphology and associated morbidities. Our ability to prevent or mitigate craniofacial skeletal anomalies is at least partly dependent on our understanding of the unique physiological development of the craniofacial skeleton. Mouse models are critical tools for the study of craniofacial developmental abnormalities. However, there is a lack of detailed normative data of mouse craniofacial skeletal development in the literature. In this report, we employed high-resolution micro-computed tomography (μCT) in combination with morphometric measurements to analyze the postnatal craniofacial skeletal development from day 7 (P7) through day 390 (P390) of female C57BL/6NCrl mice, a widely used mouse strain. Our data demonstrates a unique craniofacial skeletal development pattern in female C57BL/6NCrl mice, and differentiates the early vs. late craniofacial growth patterns. Additionally, our data documents the complex and differential changes in bone parameters (thickness, bone volume, bone volume/tissue volume, bone mineral density, and tissue mineral density) of various craniofacial bones with different embryonic origins and ossification mechanisms during postnatal growth, which underscores the complexity of craniofacial bone development and provides a reference standard for future quantitative analysis of craniofacial bones.},
|
||||||
|
pmid = {28959213},
|
||||||
|
doi = {10.3389/fphys.2017.00697},
|
||||||
|
pmc = {PMC5603710},
|
||||||
|
url = {papers/Wei_FrontPhysiol2020-28959213.pdf},
|
||||||
|
nlmuniqueid = {101549006}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{Xiong2017,
|
||||||
|
title = {Precise Cerebral Vascular Atlas in Stereotaxic Coordinates of Whole Mouse Brain.},
|
||||||
|
author = {Xiong, Benyi and Li, Anan and Lou, Yang and Chen, Shangbin and Long, Ben and Peng, Jie and Yang, Zhongqin and Xu, Tonghui and Yang, Xiaoquan and Li, Xiangning and Jiang, Tao and Luo, Qingming and Gong, Hui},
|
||||||
|
journal = {Front Neuroanat},
|
||||||
|
volume = {11},
|
||||||
|
year = {2017},
|
||||||
|
pages = {128},
|
||||||
|
abstract = {Understanding amazingly complex brain functions and pathologies requires a complete cerebral vascular atlas in stereotaxic coordinates. Making a precise atlas for cerebral arteries and veins has been a century-old objective in neuroscience and neuropathology. Using micro-optical sectioning tomography (MOST) with a modified Nissl staining method, we acquired five mouse brain data sets containing arteries, veins, and microvessels. Based on the brain-wide vascular spatial structures and brain regions indicated by cytoarchitecture in one and the same mouse brain, we reconstructed and annotated the vascular system atlas of both arteries and veins of the whole mouse brain for the first time. The distributing patterns of the vascular system within the brain regions were acquired and our results show that the patterns of individual vessels are different from each other. Reconstruction and statistical analysis of the microvascular network, including derivation of quantitative vascular densities, indicate significant differences mainly in vessels with diameters less than 8 μm and large than 20 μm across different brain regions. Our precise cerebral vascular atlas provides an important resource and approach for quantitative studies of brain functions and diseases.},
|
||||||
|
pmid = {29311856},
|
||||||
|
doi = {10.3389/fnana.2017.00128},
|
||||||
|
pmc = {PMC5742197},
|
||||||
|
url = {papers/Xiong_FrontNeuroanat2020-29311856.pdf},
|
||||||
|
nlmuniqueid = {101477943}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{Richiardi2013,
|
||||||
|
author={Richiardi, Jonas and Achard, Sophie and Bunke, Horst and Van De Ville, Dimitri},
|
||||||
|
journal={IEEE Signal Processing Magazine},
|
||||||
|
title={Machine Learning with Brain Graphs: Predictive Modeling Approaches for Functional Imaging in Systems Neuroscience},
|
||||||
|
year={2013},
|
||||||
|
volume={30},
|
||||||
|
number={3},
|
||||||
|
pages={58-70},
|
||||||
|
abstract={The observation and description of the living brain has attracted a lot of research over the past centuries. Many noninvasive imaging modalities have been developed, such as topographical techniques based on the electromagnetic field potential [i.e., electroencephalography (EEG) and magnetoencephalography (MEG)], and tomography approaches including positron emission tomography and magnetic resonance imaging (MRI). Here we will focus on functional MRI (fMRI) since it is widely deployed for clinical and cognitive neurosciences today, and it can reveal brain function due to neurovascular coupling (see ?From Brain Images to fMRI Time Series?). It has led to a much better understanding of brain function, including the description of brain areas with very specialized functions such as face recognition. These neuroscientific insights have been made possible by important methodological advances in MR physics, signal processing, and mathematical modeling.},
|
||||||
|
keywords={},
|
||||||
|
doi={10.1109/MSP.2012.2233865},
|
||||||
|
ISSN={1558-0792},
|
||||||
|
month={May},
|
||||||
|
url = {papers/Richiardi_IEEESigProc2013.pdf}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{Torrence1998,
|
||||||
|
author = {Torrence, Christopher and Compo, Gilbert P.},
|
||||||
|
title = {A Practical Guide to Wavelet Analysis},
|
||||||
|
journal = {Bulletin of the American Meteorological Society},
|
||||||
|
year = {1998},
|
||||||
|
publisher = {American Meteorological Society},
|
||||||
|
address = {Boston MA, USA},
|
||||||
|
volume = {79},
|
||||||
|
number = {1},
|
||||||
|
doi = {10.1175/1520-0477(1998)079<0061:APGTWA>2.0.CO;2},
|
||||||
|
pages= {61 - 78},
|
||||||
|
url = {papers/Torrence_BulletinAMS1998.pdf}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{Virtanen2020,
|
||||||
|
title = {SciPy 1.0: fundamental algorithms for scientific computing in Python.},
|
||||||
|
author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and van der Walt, Stéfan J and Brett, Matthew and Wilson, Joshua and Millman, K Jarrod and Mayorov, Nikolay and Nelson, Andrew R J and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C J and Polat, İlhan and Feng, Yu and Moore, Eric W and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E A and Harris, Charles R and Archibald, Anne M and Ribeiro, Antônio H and Pedregosa, Fabian and van Mulbregt, Paul and , },
|
||||||
|
journal = {Nat Methods},
|
||||||
|
volume = {17},
|
||||||
|
number = {3},
|
||||||
|
year = {2020},
|
||||||
|
month = {03},
|
||||||
|
pages = {261-272},
|
||||||
|
abstract = {SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.},
|
||||||
|
keywords = {Algorithms; Computational Biology; Computer Simulation; History, 20th Century; History, 21st Century; Linear Models; Models, Biological; Nonlinear Dynamics; Programming Languages; Signal Processing, Computer-Assisted; Software; },
|
||||||
|
pmid = {32015543},
|
||||||
|
doi = {10.1038/s41592-019-0686-2},
|
||||||
|
pii = {10.1038/s41592-019-0686-2},
|
||||||
|
pmc = {PMC7056644},
|
||||||
|
url = {papers/Virtanen_NatMethods2020-32015543.pdf},
|
||||||
|
nlmuniqueid = {101215604}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{Abraham2014,
|
||||||
|
title = {Machine learning for neuroimaging with scikit-learn.},
|
||||||
|
author = {Abraham, Alexandre and Pedregosa, Fabian and Eickenberg, Michael and Gervais, Philippe and Mueller, Andreas and Kossaifi, Jean and Gramfort, Alexandre and Thirion, Bertrand and Varoquaux, Gaël},
|
||||||
|
journal = {Front Neuroinform},
|
||||||
|
volume = {8},
|
||||||
|
year = {2014},
|
||||||
|
pages = {14},
|
||||||
|
abstract = {Statistical machine learning methods are increasingly used for neuroimaging data analysis. Their main virtue is their ability to model high-dimensional datasets, e.g., multivariate analysis of activation images or resting-state time series. Supervised learning is typically used in decoding or encoding settings to relate brain images to behavioral or clinical observations, while unsupervised learning can uncover hidden structures in sets of images (e.g., resting state functional MRI) or find sub-populations in large cohorts. By considering different functional neuroimaging applications, we illustrate how scikit-learn, a Python machine learning library, can be used to perform some key analysis steps. Scikit-learn contains a very large set of statistical learning algorithms, both supervised and unsupervised, and its application to neuroimaging data provides a versatile tool to study the brain. },
|
||||||
|
pmid = {24600388},
|
||||||
|
doi = {10.3389/fninf.2014.00014},
|
||||||
|
pmc = {PMC3930868},
|
||||||
|
url = {papers/Abraham_FrontNeuroinform2014-24600388.pdf},
|
||||||
|
nlmuniqueid = {101477957}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{Pedregosa2011,
|
||||||
|
author = {Pedregosa, Fabian and Varoquaux, Ga\"{e}l and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, \'{E}douard},
|
||||||
|
title = {Scikit-Learn: Machine Learning in Python},
|
||||||
|
year = {2011},
|
||||||
|
issue_date = {2/1/2011},
|
||||||
|
publisher = {JMLR.org},
|
||||||
|
volume = {12},
|
||||||
|
number = {null},
|
||||||
|
issn = {1532-4435},
|
||||||
|
abstract = {Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.sourceforge.net.},
|
||||||
|
journal = {J. Mach. Learn. Res.},
|
||||||
|
month = {nov},
|
||||||
|
pages = {2825–2830},
|
||||||
|
numpages = {6},
|
||||||
|
doi = {10.5555/1953048.2078195},
|
||||||
|
url = {papers/Pedregosa_JMLR2011.pdf}
|
||||||
|
}
|
||||||
|
|
||||||
|
@book{Geron2017,
|
||||||
|
author = {Géron, Aurélien},
|
||||||
|
isbn = {978-1491962299},
|
||||||
|
publisher = {O'Reilly},
|
||||||
|
title = {Hands-On Machine Learning with Scikit-Learn and TensorFlow},
|
||||||
|
year = {2017}
|
||||||
|
}
|
||||||
|
|||||||
Reference in New Issue
Block a user