refy/example_library.bib

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@ARTICLE{Mizumori2005-mq,
  title     = "Head direction codes in hippocampal afferent and efferent
               systems: what functions do they serve",
  author    = "Mizumori, Sheri J Y and Puryear, Corey B and Gill, Kathryn M and
               Guazzelli, Alex",
  abstract  = "The discovery of head direction cells in many limbic and
               limbic-afferent structures could lead one to suggest that the
               limbic system is specialized for spatial analysis, and in
               particular the processing of directional orientation.
               Considering this hypothesis, it becomes important to know
               whether head direction codes are unique to the limbic system.
               Previous chapters provide convincing evidence that the mechanism
               for the generation of head direction signals involves sequential
               processing through the tegmentum, mammillary nucleus, anterior
               dorsal …",
  journal   = "Head direction cells and the neural mechanisms of spatial
               orientation",
  publisher = "books.google.com",
  pages     = "203--220",
  year      =  2005
}

@ARTICLE{Melzer2017-ek,
  title     = "Distinct Corticostriatal {GABAergic} Neurons Modulate Striatal
               Output Neurons and Motor Activity",
  author    = "Melzer, Sarah and Gil, Mariana and Koser, David E and Michael,
               Magdalena and Huang, Kee Wui and Monyer, Hannah",
  abstract  = "The motor cortico-basal ganglion loop is critical for motor
               planning, execution, and learning. Balanced excitation and
               inhibition in this loop is crucial for proper motor output.
               Excitatory neurons have been thought to be the only source of
               motor cortical input to the striatum. Here, we identify
               long-range projecting GABAergic neurons in the primary (M1) and
               secondary (M2) motor cortex that target the dorsal striatum.
               This population of projecting GABAergic neurons comprises both
               somatostatin-positive (SOM+) and parvalbumin-positive (PV+)
               neurons that target direct and indirect pathway striatal output
               neurons as well as cholinergic interneurons differentially.
               Notably, optogenetic stimulation of M1 PV+ and M2 SOM+
               projecting neurons reduced locomotion, whereas stimulation of M1
               SOM+ projecting neurons enhanced locomotion. Thus,
               corticostriatal GABAergic projections modulate striatal output
               and motor activity.",
  journal   = "Cell Rep.",
  publisher = "Elsevier",
  volume    =  19,
  number    =  5,
  pages     = "1045--1055",
  month     =  may,
  year      =  2017,
  keywords  = "GABA; locomotion; long-range; motor cortex; optogenetics;
               parvalbumin; somatostatin; striatum;Locomotion",
  language  = "en",
  issn      = "2211-1247",
  pmid      = "28467898",
  doi       = "10.1016/j.celrep.2017.04.024",
  pmc       = "PMC5437725"
}



@ARTICLE{Murakami2014-lh,
  title     = "Neural antecedents of self-initiated actions in secondary motor
               cortex",
  author    = "Murakami, Masayoshi and Vicente, M In{\^e}s and Costa, Gil M and
               Mainen, Zachary F",
  abstract  = "The neural origins of spontaneous or self-initiated actions are
               not well understood and their interpretation is controversial.
               To address these issues, we used a task in which rats decide
               when to abort waiting for a delayed tone. We recorded neurons in
               the secondary motor cortex (M2) and interpreted our findings in
               light of an integration-to-bound decision model. A first
               population of M2 neurons ramped to a constant threshold at rates
               proportional to waiting time, strongly resembling integrator
               output. A second population, which we propose provide input to
               the integrator, fired in sequences and showed trial-to-trial
               rate fluctuations correlated with waiting times. An integration
               model fit to these data also quantitatively predicted the
               observed inter-neuronal correlations. Together, these results
               reinforce the generality of the integration-to-bound model of
               decision-making. These models identify the initial intention to
               act as the moment of threshold crossing while explaining how
               antecedent subthreshold neural activity can influence an action
               without implying a decision.",
  journal   = "Nat. Neurosci.",
  publisher = "nature.com",
  volume    =  17,
  number    =  11,
  pages     = "1574--1582",
  month     =  nov,
  year      =  2014,
  language  = "en",
  issn      = "1097-6256, 1546-1726",
  pmid      = "25262496",
  doi       = "10.1038/nn.3826"
}

@ARTICLE{Gremel2013-im,
  title     = "Premotor cortex is critical for goal-directed actions",
  author    = "Gremel, Christina M and Costa, Rui M",
  abstract  = "Shifting between motor plans is often necessary for adaptive
               behavior. When faced with changing consequences of one's
               actions, it is often imperative to switch from automatic actions
               to deliberative and controlled actions. The pre-supplementary
               motor area (pre-SMA) in primates, akin to the premotor cortex
               (M2) in mice, has been implicated in motor learning and
               planning, and action switching. We hypothesized that M2 would be
               differentially involved in goal-directed actions, which are
               controlled by their consequences vs. habits, which are more
               dependent on their past reinforcement history and less on their
               consequences. To investigate this, we performed M2 lesions in
               mice and then concurrently trained them to press the same lever
               for the same food reward using two different schedules of
               reinforcement that differentially bias towards the use of
               goal-directed versus habitual action strategies. We then probed
               whether actions were dependent on their expected consequence
               through outcome revaluation testing. We uncovered that M2
               lesions did not affect the acquisition of lever-pressing.
               However, in mice with M2 lesions, lever-pressing was insensitive
               to changes in expected outcome value following goal-directed
               training. However, habitual actions were intact. We confirmed a
               role for M2 in goal-directed but not habitual actions in
               separate groups of mice trained on the individual schedules
               biasing towards goal-directed versus habitual actions. These
               data indicate that M2 is critical for actions to be updated
               based on their consequences, and suggest that habitual action
               strategies may not require processing by M2 and the updating of
               motor plans.",
  journal   = "Front. Comput. Neurosci.",
  publisher = "frontiersin.org",
  volume    =  7,
  pages     = "110",
  month     =  aug,
  year      =  2013,
  keywords  = "action selection; goal-directed actions; habitual actions;
               premotor cortex; value-based decision making",
  language  = "en",
  issn      = "1662-5188",
  pmid      = "23964233",
  doi       = "10.3389/fncom.2013.00110",
  pmc       = "PMC3740264"
}

@ARTICLE{Erlich2011-rn,
  title     = "A cortical substrate for memory-guided orienting in the rat",
  author    = "Erlich, Jeffrey C and Bialek, Max and Brody, Carlos D",
  abstract  = "Anatomical, stimulation, and lesion data have suggested a
               homology between the rat frontal orienting fields (FOF)
               (centered at +2 AP, $\pm$1.3 ML mm from Bregma) and primate
               frontal cortices such as the frontal or supplementary eye
               fields. We investigated the functional role of the FOF using
               rats trained to perform a memory-guided orienting task, in which
               there was a delay period between the end of a sensory stimulus
               instructing orienting direction and the time of the allowed
               motor response. Unilateral inactivation of the FOF resulted in
               impaired contralateral responses. Extracellular recordings of
               single units revealed that 37\% of FOF neurons had delay period
               firing rates that predicted the direction of the rats' later
               orienting motion. Our data provide the first
               electrophysiological and pharmacological evidence supporting the
               existence in the rat, as in the primate, of a frontal cortical
               area involved in the preparation and/or planning of orienting
               responses.",
  journal   = "Neuron",
  publisher = "Elsevier",
  volume    =  72,
  number    =  2,
  pages     = "330--343",
  month     =  oct,
  year      =  2011,
  keywords  = "To Read;navigation",
  language  = "en",
  issn      = "0896-6273, 1097-4199",
  pmid      = "22017991",
  doi       = "10.1016/j.neuron.2011.07.010",
  pmc       = "PMC3212026"
}

@ARTICLE{Jeong2016-dq,
  title    = "Comparative three-dimensional connectome map of motor cortical
              projections in the mouse brain",
  author   = "Jeong, Minju and Kim, Yongsoo and Kim, Jeongjin and Ferrante,
              Daniel D and Mitra, Partha P and Osten, Pavel and Kim, Daesoo",
  abstract = "The motor cortex orchestrates simple to complex motor behaviors
              through its output projections to target areas. The primary (MOp)
              and secondary (MOs) motor cortices are known to produce specific
              output projections that are targeted to both similar and
              different target areas. These projections are further divided
              into layer 5 and 6 neuronal outputs, thereby producing four
              cortical outputs that may target other areas in a combinatorial
              manner. However, the precise network structure that integrates
              these four projections remains poorly understood. Here, we
              constructed a whole-brain, three-dimensional (3D) map showing the
              tract pathways and targeting locations of these four motor
              cortical outputs in mice. Remarkably, these motor cortical
              projections showed unique and separate tract pathways despite
              targeting similar areas. Within target areas, various
              combinations of these four projections were defined based on
              specific 3D spatial patterns, reflecting anterior-posterior,
              dorsal-ventral, and core-capsular relationships. This 3D
              topographic map ultimately provides evidence for the relevance of
              comparative connectomics: motor cortical projections known to be
              convergent are actually segregated in many target areas with
              unique targeting patterns, a finding that has anatomical value
              for revealing functional subdomains that have not been classified
              by conventional methods.",
  journal  = "Sci. Rep.",
  volume   =  6,
  pages    = "20072",
  month    =  feb,
  year     =  2016,
  keywords = "To Read",
  language = "en",
  issn     = "2045-2322",
  pmid     = "26830143",
  doi      = "10.1038/srep20072",
  pmc      = "PMC4735720"
}

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@ARTICLE{Gradinaru2007-qv,
  title     = "Targeting and readout strategies for fast optical neural control
               in vitro and in vivo",
  author    = "Gradinaru, Viviana and Thompson, Kimberly R and Zhang, Feng and
               Mogri, Murtaza and Kay, Kenneth and Schneider, M Bret and
               Deisseroth, Karl",
  abstract  = "Major obstacles faced by neuroscientists in attempting to
               unravel the complexity of brain function include both the
               heterogeneity of brain tissue (with a multitude of cell types
               present in vivo) and the high speed of brain information
               processing (with behaviorally relevant millisecondscale
               electrical activity patterns). To address different aspects of
               these technical constraints, genetically targetable neural
               modulation tools have been developed by a number of groups
               (Zemelman et al., 2002; Banghart et al., 2004; Karpova et al.,
               2005; Lima …",
  journal   = "J. Neurosci.",
  publisher = "Soc Neuroscience",
  volume    =  27,
  number    =  52,
  pages     = "14231--14238",
  month     =  dec,
  year      =  2007,
  keywords  = "Locomotion",
  language  = "en",
  issn      = "0270-6474, 1529-2401",
  pmid      = "18160630",
  doi       = "10.1523/JNEUROSCI.3578-07.2007",
  pmc       = "PMC6673457"
}

@ARTICLE{Magno2019-qz,
  title    = "Optogenetic Stimulation of the {M2} Cortex Reverts Motor
              Dysfunction in a Mouse Model of Parkinson's Disease",
  author   = "Magno, Luiz Alexandre Viana and Tenza-Ferrer, Helia and
              Collodetti, M{\'e}lcar and Aguiar, Matheus Felipe Guimar{\~a}es
              and Rodrigues, Ana Paula Carneiro and da Silva, Rodrigo Souza and
              Silva, Joice do Prado and Nicolau, Nycolle Ferreira and Rosa,
              Daniela Valad{\~a}o Freitas and Birbrair, Alexander and Miranda,
              D{\'e}bora Marques and Romano-Silva, Marco Aur{\'e}lio",
  abstract = "Neuromodulation of deep brain structures (deep brain stimulation)
              is the current surgical procedure for treatment of Parkinson's
              disease (PD). Less studied is the stimulation of cortical motor
              areas to treat PD symptoms, although also known to alleviate
              motor disturbances in PD. We were able to show that optogenetic
              activation of secondary (M2) motor cortex improves motor
              functions in dopamine-depleted male mice. The stimulated M2
              cortex harbors glutamatergic pyramidal neurons that project to
              subcortical structures, critically involved in motor control, and
              makes synaptic contacts with dopaminergic neurons. Strikingly,
              optogenetic activation of M2 neurons or axons into the
              dorsomedial striatum increases striatal levels of dopamine and
              evokes locomotor activity. We found that dopamine
              neurotransmission sensitizes the locomotor behavior elicited by
              activation of M2 neurons. Furthermore, combination of intranigral
              infusion of glutamatergic antagonists and circuit specific
              optogenetic stimulation revealed that behavioral response
              depended on the activity of M2 neurons projecting to SNc.
              Interestingly, repeated M2 stimulation combined with l-DOPA
              treatment produced an unanticipated improvement in working memory
              performance, which was absent in control mice under l-DOPA
              treatment only. Therefore, the M2-basal ganglia circuit is
              critical for the assembly of the motor and cognitive function,
              and this study demonstrates a therapeutic mechanism for cortical
              stimulation in PD that involves recruitment of long-range
              glutamatergic projection neurons.SIGNIFICANCE STATEMENT Some
              patients with Parkinson's disease are offered treatment through
              surgery, which consists of delivering electrical current to
              regions deep within the brain. This study shows that stimulation
              of an area located on the brain surface, known as the secondary
              motor cortex, can also reverse movement disorders in mice.
              Authors have used a brain stimulation technique called
              optogenetics, which allowed targeting a specific type of surface
              neuron that communicates with the deep part of the brain involved
              in movement control. The study also shows that a combination of
              this stimulation with drug treatment might be useful to treat
              memory impairment, a kind of cognitive problem in Parkinson's
              disease.",
  journal  = "J. Neurosci.",
  volume   =  39,
  number   =  17,
  pages    = "3234--3248",
  month    =  apr,
  year     =  2019,
  keywords = "Parkinson's disorder; brain stimulation; cognition; movement;
              optogenetics; prefrontal cortex;Locomotion",
  language = "en",
  issn     = "0270-6474, 1529-2401",
  pmid     = "30782975",
  doi      = "10.1523/JNEUROSCI.2277-18.2019",
  pmc      = "PMC6788829"
}

@ARTICLE{Schiemann2015-th,
  title     = "Cellular mechanisms underlying behavioral state-dependent
               bidirectional modulation of motor cortex output",
  author    = "Schiemann, Julia and Puggioni, Paolo and Dacre, Joshua and
               Pelko, Miha and Domanski, Aleksander and van Rossum, Mark C W
               and Duguid, Ian",
  abstract  = "Neuronal activity in primary motor cortex (M1) correlates with
               behavioral state, but the cellular mechanisms underpinning
               behavioral state-dependent modulation of M1 output remain
               largely unresolved. Here, we performed in vivo patch-clamp
               recordings from layer 5B (L5B) pyramidal neurons in awake mice
               during quiet wakefulness and self-paced, voluntary movement. We
               show that L5B output neurons display bidirectional (i.e.,
               enhanced or suppressed) firing rate changes during movement,
               mediated via two opposing subthreshold mechanisms: (1) a global
               decrease in membrane potential variability that reduced L5B
               firing rates (L5Bsuppressed neurons), and (2) a coincident
               noradrenaline-mediated increase in excitatory drive to a
               subpopulation of L5B neurons (L5Benhanced neurons) that elevated
               firing rates. Blocking noradrenergic receptors in forelimb M1
               abolished the bidirectional modulation of M1 output during
               movement and selectively impaired contralateral forelimb motor
               coordination. Together, our results provide a mechanism for how
               noradrenergic neuromodulation and network-driven input changes
               bidirectionally modulate M1 output during motor behavior.",
  journal   = "Cell Rep.",
  publisher = "Elsevier",
  volume    =  11,
  number    =  8,
  pages     = "1319--1330",
  month     =  may,
  year      =  2015,
  keywords  = "To Read",
  language  = "en",
  issn      = "2211-1247",
  pmid      = "25981037",
  doi       = "10.1016/j.celrep.2015.04.042",
  pmc       = "PMC4451462"
}

@ARTICLE{Ebbesen2017-cm,
  title    = "Motor cortex - to act or not to act?",
  author   = "Ebbesen, Christian Laut and Brecht, Michael",
  abstract = "The motor cortex is a large frontal structure in the cerebral
              cortex of eutherian mammals. A vast array of evidence implicates
              the motor cortex in the volitional control of motor output, but
              how does the motor cortex exert this 'control'? Historically,
              ideas regarding motor cortex function have been shaped by the
              discovery of cortical 'motor maps' - that is, ordered
              representations of stimulation-evoked movements in anaesthetized
              animals. Volitional control, however, entails the initiation of
              movements and the ability to suppress undesired movements. In
              this article, we highlight classic and recent findings that
              emphasize that motor cortex neurons have a role in both
              processes.",
  journal  = "Nat. Rev. Neurosci.",
  volume   =  18,
  number   =  11,
  pages    = "694--705",
  month    =  oct,
  year     =  2017,
  language = "en",
  issn     = "1471-003X, 1471-0048",
  pmid     = "29042690",
  doi      = "10.1038/nrn.2017.119"
}

@ARTICLE{Calton2009-hj,
  title    = "Where am {I} and how will {I} get there from here? A role for
              posterior parietal cortex in the integration of spatial
              information and route planning",
  author   = "Calton, Jeffrey L and Taube, Jeffrey S",
  abstract = "The ability of an organism to accurately navigate from one place
              to another requires integration of multiple spatial constructs,
              including the determination of one's position and direction in
              space relative to allocentric landmarks, movement velocity, and
              the perceived location of the goal of the movement. In this
              review, we propose that while limbic areas are important for the
              sense of spatial orientation, the posterior parietal cortex is
              responsible for relating this sense with the location of a
              navigational goal and in formulating a plan to attain it. Hence,
              the posterior parietal cortex is important for the computation of
              the correct trajectory or route to be followed while navigating.
              Prefrontal and motor areas are subsequently responsible for
              executing the planned movement. Using this theory, we are able to
              bridge the gap between the rodent and primate literatures by
              suggesting that the allocentric role of the rodent PPC is largely
              analogous to the egocentric role typically emphasized in
              primates, that is, the integration of spatial orientation with
              potential goals in the planning of goal-directed movements.",
  journal  = "Neurobiol. Learn. Mem.",
  volume   =  91,
  number   =  2,
  pages    = "186--196",
  month    =  feb,
  year     =  2009,
  keywords = "navigation;To Read",
  language = "en",
  issn     = "1074-7427, 1095-9564",
  pmid     = "18929674",
  doi      = "10.1016/j.nlm.2008.09.015",
  pmc      = "PMC2666283"
}

@ARTICLE{Cho2001-nw,
  title     = "Head direction, place, and movement correlates for cells in the
               rat retrosplenial cortex",
  author    = "Cho, J and Sharp, P E",
  abstract  = "The retrosplenial cortex is strongly connected with brain
               regions involved in spatial signaling. To test whether it also
               codes space, single cells were recorded while rats navigated in
               an open field. As in earlier work (L. L. Chen, L. H. Lin, C. A.
               Barnes, \& B. L. McNaughton, 1994; L. L. Chen, L. H. Lin, E. J.
               Green, C. A. Barnes, \& B. L. McNaughton, 1994), the authors
               found head direction cells with properties similar to those in
               other areas. These cells were slightly anticipatory. Another
               cell type fired to particular combinations of location,
               direction, and movement, which suggested that they may fire
               whenever the rat approaches a particular location, using a
               particular locomotor behavior. The remaining cells could not be
               clearly categorized but also showed a significant correlation
               with one or more of the spatial-movement variables examined. The
               fact that the retrosplenial cortex contains spatial and
               movement-related signals and is connected with the motor cortex
               suggests that it may play a role in path integration or
               navigational motor planning.",
  journal   = "Behav. Neurosci.",
  publisher = "psycnet.apa.org",
  volume    =  115,
  number    =  1,
  pages     = "3--25",
  month     =  feb,
  year      =  2001,
  keywords  = "navigation;To Read",
  language  = "en",
  issn      = "0735-7044",
  pmid      = "11256450",
  doi       = "10.1037/0735-7044.115.1.3"
}

@ARTICLE{Li2015-tj,
  title    = "A motor cortex circuit for motor planning and movement",
  author   = "Li, Nuo and Chen, Tsai-Wen and Guo, Zengcai V and Gerfen, Charles
              R and Svoboda, Karel",
  abstract = "Activity in motor cortex predicts specific movements seconds
              before they occur, but how this preparatory activity relates to
              upcoming movements is obscure. We dissected the conversion of
              preparatory activity to movement within a structured motor cortex
              circuit. An anterior lateral region of the mouse cortex (a
              possible homologue of premotor cortex in primates) contains equal
              proportions of intermingled neurons predicting ipsi- or
              contralateral movements, yet unilateral inactivation of this
              cortical region during movement planning disrupts contralateral
              movements. Using cell-type-specific electrophysiology, cellular
              imaging and optogenetic perturbation, we show that layer 5
              neurons projecting within the cortex have unbiased laterality.
              Activity with a contralateral population bias arises specifically
              in layer 5 neurons projecting to the brainstem, and only late
              during movement planning. These results reveal the transformation
              of distributed preparatory activity into movement commands within
              hierarchically organized cortical circuits.",
  journal  = "Nature",
  volume   =  519,
  number   =  7541,
  pages    = "51--56",
  month    =  mar,
  year     =  2015,
  keywords = "To Read",
  language = "en",
  issn     = "0028-0836, 1476-4687",
  pmid     = "25731172",
  doi      = "10.1038/nature14178"
}

@ARTICLE{McNaughton1994-hv,
  title    = "Cortical representation of motion during unrestrained spatial
              navigation in the rat",
  author   = "McNaughton, B L and Mizumori, S J and Barnes, C A and Leonard, B
              J and Marquis, M and Green, E J",
  abstract = "Neural activity related to unrestrained movement through space
              was studied in rat sensorimotor and posterior parietal cortices
              during performance of an eight-arm, radial maze task. Nearly half
              of the cells exhibited movement-related activity that
              discriminated among three basic modes of locomotion: left turns,
              right turns, and forward motion. Correlates ranged from strong
              excitation (relative to the still condition) to strong
              inhibition, and were distributed among the movement modes in a
              variety of different ways. For example, cells that discriminated
              between clockwise and counterclockwise turns did so with either
              antagonistic responses or simple excitation or inhibition. Others
              showed either excitation or inhibition relative to both turning
              and the still condition, and hence were selective for forward
              motion. Many cells exhibited somatosensory responsiveness;
              however, in agreement with findings of others, motion correlates
              could rarely be sensibly explained by the somatosensory response.
              Moreover, movement correlates sometimes varied considerably with
              spatial context. Some cells exhibited more complex motion
              correlates, such as an apparent dependence on the nature of the
              preceding movement. Irrespective of the specific sensory or motor
              determinants of cell activity, which varied considerably among
              cells, the posterior neocortex of the rat appears to generate a
              robust and redundant internal representation of body motion
              through space. Such a representation could be useful in
              constructing ``cognitive maps'' of the environment.",
  journal  = "Cereb. Cortex",
  volume   =  4,
  number   =  1,
  pages    = "27--39",
  month    =  jan,
  year     =  1994,
  keywords = "navigation",
  language = "en",
  issn     = "1047-3211",
  pmid     = "8180489",
  doi      = "10.1093/cercor/4.1.27"
}

@ARTICLE{Kiehn2006-wi,
  title     = "Locomotor circuits in the mammalian spinal cord",
  author    = "Kiehn, Ole",
  abstract  = "Intrinsic spinal networks, known as central pattern generators
               (CPGs), control the timing and pattern of the muscle activity
               underlying locomotion in mammals. This review discusses new
               advances in understanding the mammalian CPGs with a focus on
               experiments that address the overall network structure as well
               as the identification of CPG neurons. I address the
               identification of excitatory CPG neurons and their role in
               rhythm generation, the organization of flexor-extensor networks,
               and the diverse role of commissural interneurons in coordinating
               left-right movements. Molecular and genetic approaches that have
               the potential to elucidate the function of populations of CPG
               interneurons are also discussed.",
  journal   = "Annu. Rev. Neurosci.",
  publisher = "annualreviews.org",
  volume    =  29,
  pages     = "279--306",
  year      =  2006,
  keywords  = "Locomotion",
  language  = "en",
  issn      = "0147-006X",
  pmid      = "16776587",
  doi       = "10.1146/annurev.neuro.29.051605.112910"
}

@ARTICLE{Fukuoka2015-ks,
  title    = "A simple rule for quadrupedal gait generation determined by leg
              loading feedback: a modeling study",
  author   = "Fukuoka, Yasuhiro and Habu, Yasushi and Fukui, Takahiro",
  abstract = "We discovered a specific rule for generating typical quadrupedal
              gaits (the order of the movement of four legs) through a
              simulated quadrupedal locomotion, in which unprogrammed gaits
              (diagonal/lateral sequence walks, left/right-lead canters, and
              left/right-lead transverse gallops) spontaneously emerged because
              of leg loading feedbacks to the CPGs hard-wired to produce a
              default trot. Additionally, all gaits transitioned according to
              speed, as seen in animals. We have therefore hypothesized that
              various gaits derive from a trot because of posture control
              through leg loading feedback. The body tilt on the two support
              legs of each diagonal pair during trotting was classified into
              three types (level, tilted up, or tilted down) according to
              speed. The load difference between the two legs led to the phase
              difference between their CPGs via the loading feedbacks,
              resulting in nine gaits (3(2): three tilts to the power of two
              diagonal pairs) including the aforementioned.",
  journal  = "Sci. Rep.",
  volume   =  5,
  pages    = "8169",
  month    =  feb,
  year     =  2015,
  keywords = "Locomotion",
  language = "en",
  issn     = "2045-2322",
  pmid     = "25639661",
  doi      = "10.1038/srep08169",
  pmc      = "PMC4313093"
}

@UNPUBLISHED{Roseberry2019-iz,
  title    = "Locomotor suppression by a monosynaptic amygdala to brainstem
              circuit",
  author   = "Roseberry, Thomas K and Lalive, Arnaud L and Margolin, Benjamin D
              and Kreitzer, Anatol C",
  abstract = "Abstract The control of locomotion is fundamental to vertebrate
              animal survival. Defensive situations require an animal to
              rapidly decide whether to run away or suppress locomotor activity
              to avoid detection. While much of the neural circuitry involved
              in defensive action selection has been elucidated, top-down
              modulation of brainstem locomotor circuitry remains unclear. Here
              we provide evidence for the existence and functionality of a
              monosynaptic connection from the central amygdala (CeA) to the
              mesencephalic locomotor region (MLR) that inhibits locomotion in
              unconditioned and conditioned defensive behavior in mice. We show
              that locomotion stimulated by airpuff coincides with increased
              activity of MLR glutamatergic neurons. Using retrograde tracing
              and ex vivo electrophysiology, we find that the CeA makes a
              monosynaptic connection with the MLR. In the open field, in vivo
              stimulation of this projection suppressed spontaneous locomotion,
              whereas inhibition of this projection had no effect. However,
              inhibiting CeA terminals within the MLR increased both neural
              activity and locomotor responses to airpuff. Finally, using a
              conditioned avoidance paradigm known to activate CeA neurons, we
              find that inhibition of the CeA projection increased successful
              escape, whereas activating the projection reduced escape.
              Together these results provide evidence for a new circuit
              substrate influencing locomotion and defensive behaviors.",
  journal  = "Cold Spring Harbor Laboratory",
  pages    = "724252",
  month    =  aug,
  year     =  2019,
  keywords = "Locomotion",
  language = "en",
  doi      = "10.1101/724252"
}

@ARTICLE{Carvalho2020-pw,
  title    = "A Brainstem Locomotor Circuit Drives the Activity of Speed Cells
              in the Medial Entorhinal Cortex",
  author   = "Carvalho, Miguel M and Tanke, Nouk and Kropff, Emilio and Witter,
              Menno P and Moser, May-Britt and Moser, Edvard I",
  abstract = "Locomotion activates an array of sensory inputs that may help
              build the self-position map of the medial entorhinal cortex
              (MEC). In this map, speed-coding neurons are thought to
              dynamically update representations of the animal's position. A
              possible origin for the entorhinal speed signal is the
              mesencephalic locomotor region (MLR), which is critically
              involved in the activation of locomotor programs. Here, we
              describe, in rats, a circuit connecting the pedunculopontine
              tegmental nucleus (PPN) of the MLR to the MEC via the horizontal
              limb of the diagonal band of Broca (HDB). At each level of this
              pathway, locomotion speed is linearly encoded in neuronal firing
              rates. Optogenetic activation of PPN cells drives locomotion and
              modulates activity of speed-modulated neurons in HDB and MEC. Our
              results provide evidence for a pathway by which brainstem speed
              signals can reach cortical structures implicated in navigation
              and higher-order dynamic representations of space.",
  journal  = "Cell Rep.",
  volume   =  32,
  number   =  10,
  pages    = "108123",
  month    =  sep,
  year     =  2020,
  keywords = "diagonal band of Broca; medial entorhinal cortex; mesencephalic
              locomotor region; pedunculopontine tegmental nucleus; speed
              cells;Locomotion",
  language = "en",
  issn     = "2211-1247",
  pmid     = "32905779",
  doi      = "10.1016/j.celrep.2020.108123",
  pmc      = "PMC7487772"
}

@UNPUBLISHED{Dautan2020-lv,
  title    = "Modulation of motor behavior by the mesencephalic locomotor
              region",
  author   = "Dautan, Daniel and Kov{\'a}cs, Adrienn and Bayasgalan,
              Tsogbadrakh and Diaz-Acevedo, Miguel A and Pal, Balazs and
              Mena-Segovia, Juan",
  abstract = "The mesencephalic locomotor region (MLR) serves as an interface
              between higher-order motor systems and lower motor neurons. The
              excitatory module of the MLR is composed of the pedunculopontine
              nucleus (PPN) and the cuneiform nucleus (CnF), and their
              activation has been proposed to elicit different modalities of
              movement, but how the differences in connectivity and
              physiological properties explain their contributions to motor
              activity is not known. Here we report that CnF glutamatergic
              neurons are electrophysiologically homogeneous and have
              short-range axonal projections, whereas PPN glutamatergic neurons
              are heterogeneous and maintain long-range connections, most
              notably with the basal ganglia. Optogenetic activation of CnF
              neurons produced fast-onset, involuntary motor activity mediated
              by short-lasting muscle activation. In contrast, activation of
              PPN neurons produced long-lasting increases in muscle tone that
              reduced motor activity and disrupted gait. Our results thus
              reveal a differential contribution to motor behavior by the
              structures that compose the MLR. \#\#\# Competing Interest
              Statement The authors have declared no competing interest.",
  journal  = "Cold Spring Harbor Laboratory",
  pages    = "2020.06.25.172296",
  month    =  jun,
  year     =  2020,
  keywords = "Locomotion",
  language = "en",
  doi      = "10.1101/2020.06.25.172296"
}

@ARTICLE{Ruder2016-iv,
  title     = "{Long-Distance} Descending Spinal Neurons Ensure Quadrupedal
               Locomotor Stability",
  author    = "Ruder, Ludwig and Takeoka, Aya and Arber, Silvia",
  abstract  = "Locomotion is an essential animal behavior used for
               translocation. The spinal cord acts as key executing center, but
               how it coordinates many body parts located across distance
               remains poorly understood. Here we employed mouse genetic and
               viral approaches to reveal organizational principles of
               long-projecting spinal circuits and their role in quadrupedal
               locomotion. Using neurotransmitter identity, developmental
               origin, and projection patterns as criteria, we uncover that
               spinal segments controlling forelimbs and hindlimbs are
               bidirectionally connected by symmetrically organized direct
               synaptic pathways that encompass multiple genetically tractable
               neuronal subpopulations. We demonstrate that selective ablation
               of descending spinal neurons linking cervical to lumbar segments
               impairs coherent locomotion, by reducing postural stability and
               speed during exploratory locomotion, as well as perturbing
               interlimb coordination during reinforced high-speed stepping.
               Together, our results implicate a highly organized long-distance
               projection system of spinal origin in the control of postural
               body stabilization and reliability during quadrupedal
               locomotion.",
  journal   = "Neuron",
  publisher = "Elsevier",
  volume    =  92,
  number    =  5,
  pages     = "1063--1078",
  month     =  dec,
  year      =  2016,
  keywords  = "genetic identity; interlimb coordination; locomotion; motor
               control; posture; spinal cord;Locomotion",
  language  = "en",
  issn      = "0896-6273, 1097-4199",
  pmid      = "27866798",
  doi       = "10.1016/j.neuron.2016.10.032"
}

@ARTICLE{Drew2015-sv,
  title     = "Taking the next step: cortical contributions to the control of
               locomotion",
  author    = "Drew, Trevor and Marigold, Daniel S",
  abstract  = "The planning and execution of both discrete voluntary movements
               and visually guided locomotion depends on the contribution of
               multiple cortical areas. In this review, we discuss recent
               experiments that address the contribution of the posterior
               parietal cortex (PPC) and the motor cortex to the control of
               locomotion. The results from these experiments show that the PPC
               contributes to the planning of locomotion by providing an
               estimate of the position of an animal with respect to objects in
               its path. In contrast, the motor cortex contributes primarily to
               the execution of gait modifications by modulating the activity
               of groups of synergistic muscles active at different times
               during the gait cycle.",
  journal   = "Curr. Opin. Neurobiol.",
  publisher = "Elsevier",
  volume    =  33,
  pages     = "25--33",
  month     =  aug,
  year      =  2015,
  keywords  = "Locomotion",
  language  = "en",
  issn      = "0959-4388, 1873-6882",
  pmid      = "25643847",
  doi       = "10.1016/j.conb.2015.01.011"
}

@ARTICLE{Ueno2011-tt,
  title     = "Kinematic analyses reveal impaired locomotion following injury
               of the motor cortex in mice",
  author    = "Ueno, Masaki and Yamashita, Toshihide",
  abstract  = "Brain injury in the motor cortex can result in deleterious
               functional deficits of skilled and fine motor functions.
               However, in contrast to humans, the destruction of cortex and
               its descending fibers has been thought not to cause remarkable
               deficits in simple locomotion in quadropedal animals. In the
               present study, we aimed to investigate in detail how lesion of
               the sensorimotor cortex affected locomotion ability in mice
               using the KinemaTracer system, a novel video-based kinematic
               analyzer. We found that traumatic injury to the left
               sensorimotor cortex induced several apparent deficits in the
               movement of contralesional right limbs during treadmill
               locomotion. The step length of right limbs decreased, and the
               speed in the forward direction was abrogated in the swing phase.
               The coordinates and angle of each joint were also changed after
               the injury. Some of the abnormal values in these parameters
               gradually recovered near the control level. The number of
               cFos-expressing neurons following locomotion significantly
               decreased in the right side of the spinal cord in injured mice,
               suggesting a role for cortex and descending fibers in
               locomotion. In contrast, interlimb coordination did not change
               remarkably even after the injury, supporting the notion that the
               basic locomotor pattern was determined by intraspinal neural
               circuits. These results indicate that the motor cortex and its
               descending fibers regulate several aspects of fine limb movement
               during locomotion. Our findings provide practical parameters to
               assess motor deficits and recovery following cortical injury in
               mice.",
  journal   = "Exp. Neurol.",
  publisher = "Elsevier",
  volume    =  230,
  number    =  2,
  pages     = "280--290",
  month     =  aug,
  year      =  2011,
  keywords  = "Locomotion;To Read",
  language  = "en",
  issn      = "0014-4886, 1090-2430",
  pmid      = "21619878",
  doi       = "10.1016/j.expneurol.2011.05.006"
}

@ARTICLE{Holmes2006-fn,
  title     = "The Dynamics of Legged Locomotion: Models, Analyses, and
               Challenges",
  author    = "Holmes, Philip and Full, Robert J and Koditschek, Dan and
               Guckenheimer, John",
  abstract  = "Cheetahs and beetles run, dolphins and salmon swim, and bees and
               birds fly with grace and economy surpassing our technology.
               Evolution has shaped the breathtaking abilities of animals,
               leaving us the challenge of reconstructing their targets of
               control and mechanisms of dexterity. In this review we explore a
               corner of this fascinating world. We describe mathematical
               models for legged animal locomotion, focusing on rapidly running
               insects and highlighting past achievements and challenges that
               remain. Newtonian body--limb dynamics are most naturally
               formulated as piecewise-holonomic rigid body mechanical systems,
               whose constraints change as legs touch down or lift off. Central
               pattern generators and proprioceptive sensing require models of
               spiking neurons and simplified phase oscillator descriptions of
               ensembles of them. A full neuromechanical model of a running
               animal requires integration of these elements, along with
               proprioceptive feedback and models of goal-oriented sensing,
               planning, and learning. We outline relevant background material
               from biomechanics and neurobiology, explain key properties of
               the hybrid dynamical systems that underlie legged locomotion
               models, and provide numerous examples of such models, from the
               simplest, completely soluble ``peg-leg walker'' to complex
               neuromuscular subsystems that are yet to be assembled into
               models of behaving animals. This final integration in a
               tractable and illuminating model is an outstanding challenge.",
  journal   = "SIAM Rev.",
  publisher = "Society for Industrial and Applied Mathematics",
  volume    =  48,
  number    =  2,
  pages     = "207--304",
  month     =  jan,
  year      =  2006,
  keywords  = "Locomotion;To Read",
  issn      = "0036-1445",
  doi       = "10.1137/S0036144504445133"
}

@ARTICLE{Schwenkgrub2020-yl,
  title     = "Deep imaging in the brainstem reveals functional heterogeneity
               in V2a neurons controlling locomotion",
  author    = "Schwenkgrub, Joanna and Harrell, Evan R and Bathellier, Brice
               and Bouvier, Julien",
  abstract  = "V2a neurons are a genetically defined cell class that forms a
               major excitatory descending pathway from the brainstem reticular
               formation to the spinal cord. Their activation has been linked
               to the termination of locomotor activity based on broad
               optogenetic manipulations. However, because of the difficulties
               involved in accessing brainstem structures for in vivo cell
               type-specific recordings, V2a neuron function has never been
               directly observed during natural behaviors. Here, we imaged the
               activity of V2a neurons using micro-endoscopy in freely moving
               mice. We find that as many as half of the V2a neurons are
               excited at locomotion arrest and with low reliability. Other V2a
               neurons are inhibited at locomotor arrests and/or activated
               during other behaviors such as locomotion initiation or
               stationary grooming. Our results establish that V2a neurons not
               only drive stops as suggested by bulk optogenetics but also are
               stratified into subpopulations that likely contribute to diverse
               motor patterns.",
  journal   = "Sci Adv",
  publisher = "advances.sciencemag.org",
  volume    =  6,
  number    =  49,
  month     =  dec,
  year      =  2020,
  keywords  = "Locomotion",
  language  = "en",
  issn      = "2375-2548",
  pmid      = "33277252",
  doi       = "10.1126/sciadv.abc6309"
}

@ARTICLE{Lemieux2019-yc,
  title     = "Glutamatergic neurons of the gigantocellular reticular nucleus
               shape locomotor pattern and rhythm in the freely behaving mouse",
  author    = "Lemieux, Maxime and Bretzner, Frederic",
  abstract  = "Because of their intermediate position between supraspinal
               locomotor centers and spinal circuits, gigantocellular reticular
               nucleus (GRN) neurons play a key role in motor command. However,
               the functional contribution of glutamatergic GRN neurons in
               initiating, maintaining, and stopping locomotion is still
               unclear. Combining electromyographic recordings with optogenetic
               manipulations in freely behaving mice, we investigate the
               functional contribution of glutamatergic brainstem neurons of
               the GRN to motor and locomotor activity. Short-pulse
               photostimulation of one side of the glutamatergic GRN did not
               elicit locomotion but evoked distinct motor responses in flexor
               and extensor muscles at rest and during locomotion.
               Glutamatergic GRN outputs to the spinal cord appear to be gated
               according to the spinal locomotor network state. Increasing the
               duration of photostimulation increased motor and postural tone
               at rest and reset locomotor rhythm during ongoing locomotion. In
               contrast, photoinhibition impaired locomotor pattern and rhythm.
               We conclude that unilateral activation of glutamatergic GRN
               neurons triggered motor activity and modified ongoing locomotor
               pattern and rhythm.",
  journal   = "PLoS Biol.",
  publisher = "journals.plos.org",
  volume    =  17,
  number    =  4,
  pages     = "e2003880",
  month     =  apr,
  year      =  2019,
  keywords  = "Locomotion",
  language  = "en",
  issn      = "1544-9173, 1545-7885",
  pmid      = "31017885",
  doi       = "10.1371/journal.pbio.2003880",
  pmc       = "PMC6502437"
}

@ARTICLE{Karadimas2020-ub,
  title     = "Sensory cortical control of movement",
  author    = "Karadimas, Spyridon K and Satkunendrarajah, Kajana and
               Laliberte, Alex M and Ringuette, Dene and Weisspapir, Iliya and
               Li, Lijun and Gosgnach, Simon and Fehlings, Michael G",
  abstract  = "Walking in our complex environment requires continual higher
               order integrated spatiotemporal information. This information is
               processed in the somatosensory cortex, and it has long been
               presumed that it influences movement via descending tracts
               originating from the motor cortex. Here we show that neuronal
               activity in the primary somatosensory cortex tightly correlates
               with the onset and speed of locomotion in freely moving mice.
               Using optogenetics and pharmacogenetics in combination with in
               vivo and in vitro electrophysiology, we provide evidence for a
               direct corticospinal pathway from the primary somatosensory
               cortex that synapses with cervical excitatory neurons and
               modulates the lumbar locomotor network independently of the
               motor cortex and other supraspinal locomotor centers.
               Stimulation of this pathway enhances speed of locomotion, while
               inhibition decreases locomotor speed and ultimately terminates
               stepping. Our findings reveal a novel pathway for neural control
               of movement whereby the somatosensory cortex directly influences
               motor behavior, possibly in response to environmental cues.",
  journal   = "Nat. Neurosci.",
  publisher = "nature.com",
  volume    =  23,
  number    =  1,
  pages     = "75--84",
  month     =  jan,
  year      =  2020,
  keywords  = "Locomotion",
  language  = "en",
  issn      = "1097-6256, 1546-1726",
  pmid      = "31740813",
  doi       = "10.1038/s41593-019-0536-7"
}

@ARTICLE{Bouvier2015-nm,
  title    = "Descending Command Neurons in the Brainstem that Halt Locomotion",
  author   = "Bouvier, Julien and Caggiano, Vittorio and Leiras, Roberto and
              Caldeira, Vanessa and Bellardita, Carmelo and Balueva, Kira and
              Fuchs, Andrea and Kiehn, Ole",
  abstract = "The episodic nature of locomotion is thought to be controlled by
              descending inputs from the brainstem. Most studies have largely
              attributed this control to initiating excitatory signals, but
              little is known about putative commands that may specifically
              determine locomotor offset. To link identifiable brainstem
              populations to a potential locomotor stop signal, we used
              developmental genetics and considered a discrete neuronal
              population in the reticular formation: the V2a neurons. We find
              that those neurons constitute a major excitatory pathway to
              locomotor areas of the ventral spinal cord. Selective activation
              of V2a neurons of the rostral medulla stops ongoing locomotor
              activity, owing to an inhibition of premotor locomotor networks
              in the spinal cord. Moreover, inactivation of such neurons
              decreases spontaneous stopping in vivo. Therefore, the V2a ``stop
              neurons'' represent a glutamatergic descending pathway that
              favors immobility and may thus help control the episodic nature
              of locomotion.",
  journal  = "Cell",
  volume   =  163,
  number   =  5,
  pages    = "1191--1203",
  month    =  nov,
  year     =  2015,
  keywords = "Locomotion",
  language = "en",
  issn     = "0092-8674, 1097-4172",
  pmid     = "26590422",
  doi      = "10.1016/j.cell.2015.10.074",
  pmc      = "PMC4899047"
}

@ARTICLE{Caggiano2018-td,
  title    = "Midbrain circuits that set locomotor speed and gait selection",
  author   = "Caggiano, V and Leiras, R and Go{\~n}i-Erro, H and Masini, D and
              Bellardita, C and Bouvier, J and Caldeira, V and Fisone, G and
              Kiehn, O",
  abstract = "Locomotion is a fundamental motor function common to the animal
              kingdom. It is implemented episodically and adapted to
              behavioural needs, including exploration, which requires slow
              locomotion, and escape behaviour, which necessitates faster
              speeds. The control of these functions originates in brainstem
              structures, although the neuronal substrate(s) that support them
              have not yet been elucidated. Here we show in mice that speed and
              gait selection are controlled by glutamatergic excitatory neurons
              (GlutNs) segregated in two distinct midbrain nuclei: the
              cuneiform nucleus (CnF) and the pedunculopontine nucleus (PPN).
              GlutNs in both of these regions contribute to the control of
              slower, alternating-gait locomotion, whereas only GlutNs in the
              CnF are able to elicit high-speed, synchronous-gait locomotion.
              Additionally, both the activation dynamics and the input and
              output connectivity matrices of GlutNs in the PPN and the CnF
              support explorative and escape locomotion, respectively. Our
              results identify two regions in the midbrain that act in
              conjunction to select context-dependent locomotor behaviours.",
  journal  = "Nature",
  volume   =  553,
  number   =  7689,
  pages    = "455--460",
  month    =  jan,
  year     =  2018,
  keywords = "Locomotion",
  language = "en",
  issn     = "0028-0836, 1476-4687",
  pmid     = "29342142",
  doi      = "10.1038/nature25448",
  pmc      = "PMC5937258"
}

@ARTICLE{Usseglio2020-nl,
  title    = "Control of Orienting Movements and Locomotion by
              {Projection-Defined} Subsets of Brainstem V2a Neurons",
  author   = "Usseglio, Giovanni and Gatier, Edwin and Heuz{\'e}, Aur{\'e}lie
              and H{\'e}rent, Coralie and Bouvier, Julien",
  abstract = "Spatial orientation requires the execution of lateralized
              movements and a change in the animal's heading in response to
              multiple sensory modalities. While much research has focused on
              the circuits for sensory integration, chiefly to the midbrain
              superior colliculus (SC), the downstream cells and circuits that
              engage adequate motor actions have remained elusive. Furthermore,
              the mechanisms supporting trajectory changes are still
              speculative. Here, using transneuronal viral tracings in mice, we
              show that brainstem V2a neurons, a genetically defined subtype of
              glutamatergic neurons of the reticular formation, receive
              putative synaptic inputs from the contralateral SC. This makes
              them a candidate relay of lateralized orienting commands. We next
              show that unilateral optogenetic activations of brainstem V2a
              neurons in vivo evoked ipsilateral orienting-like responses of
              the head and the nose tip on stationary mice. When animals are
              walking, similar stimulations impose a transient locomotor arrest
              followed by a change of trajectory. Third, we reveal that these
              distinct motor actions are controlled by dedicated V2a subsets
              each projecting to a specific spinal cord segment, with at least
              (1) a lumbar-projecting subset whose unilateral activation
              specifically controls locomotor speed but neither impacts
              trajectory nor evokes orienting movements, and (2) a
              cervical-projecting subset dedicated to head orientation, but not
              to locomotor speed. Activating the latter subset suffices to
              steer the animals' directional heading, placing the head
              orientation as the prime driver of locomotor trajectory. V2a
              neurons and their modular organization may therefore underlie the
              orchestration of multiple motor actions during multi-faceted
              orienting behaviors.",
  journal  = "Curr. Biol.",
  volume   =  30,
  number   =  23,
  pages    = "4665--4681.e6",
  month    =  dec,
  year     =  2020,
  keywords = "V2a neurons; brainstem; circuit tracings; locomotion; motor
              control; mouse; optogenetics; orientation; reticulospinal
              neurons; spinal cord;Locomotion",
  language = "en",
  issn     = "0960-9822, 1879-0445",
  pmid     = "33007251",
  doi      = "10.1016/j.cub.2020.09.014"
}



@INCOLLECTION{Matsuyama2004-fv,
  title     = "Locomotor role of the corticoreticular--reticulospinal--spinal
               interneuronal system",
  booktitle = "Progress in Brain Research",
  author    = "Matsuyama, Kiyoji and Mori, Futoshi and Nakajima, Katsumi and
               Drew, Trevor and Aoki, Mamoru and Mori, Shigemi",
  abstract  = "In vertebrates, the descending reticulospinal pathway is the
               primary means of conveying locomotor command signals from higher
               motor centers to spinal interneuronal circuits, the latter
               including the central pattern generators for locomotion. The
               pathway is morphologically heterogeneous, being composed of
               various types of in-parallel-descending axons, which terminate
               with different arborization patterns in the spinal cord. Such
               morphology suggests that this pathway and its target spinal
               interneurons comprise varying types of functional subunits,
               which have a wide variety of functional roles, as dictated by
               command signals from the higher motor centers. Corticoreticular
               fibers are one of the major output pathways from the motor
               cortex to the brainstem. They project widely and diffusely
               within the pontomedullary reticular formation. Such a diffuse
               projection pattern seems well suited to combining and
               integrating the function of the various types of reticulospinal
               neurons, which are widely scattered throughout the
               pontomedullary reticular formation. The
               corticoreticular--reticulospinal--spinal interneuronal
               connections appear to operate as a cohesive, yet flexible,
               control system for the elaboration of a wide variety of
               movements, including those that combine goal-directed locomotion
               with other motor actions.",
  publisher = "Elsevier",
  volume    =  143,
  pages     = "239--249",
  month     =  jan,
  year      =  2004,
  keywords  = "Locomotion",
  doi       = "10.1016/S0079-6123(03)43024-0"
}


@ARTICLE{Maheswaranathan2020-fy,
  title         = "How recurrent networks implement contextual processing in
                   sentiment analysis",
  author        = "Maheswaranathan, Niru and Sussillo, David",
  abstract      = "Neural networks have a remarkable capacity for contextual
                   processing--using recent or nearby inputs to modify
                   processing of current input. For example, in natural
                   language, contextual processing is necessary to correctly
                   interpret negation (e.g. phrases such as ``not bad'').
                   However, our ability to understand how networks process
                   context is limited. Here, we propose general methods for
                   reverse engineering recurrent neural networks (RNNs) to
                   identify and elucidate contextual processing. We apply these
                   methods to understand RNNs trained on sentiment
                   classification. This analysis reveals inputs that induce
                   contextual effects, quantifies the strength and timescale of
                   these effects, and identifies sets of these inputs with
                   similar properties. Additionally, we analyze contextual
                   effects related to differential processing of the beginning
                   and end of documents. Using the insights learned from the
                   RNNs we improve baseline Bag-of-Words models with simple
                   extensions that incorporate contextual modification,
                   recovering greater than 90\% of the RNN's performance
                   increase over the baseline. This work yields a new
                   understanding of how RNNs process contextual information,
                   and provides tools that should provide similar insight more
                   broadly.",
  month         =  apr,
  year          =  2020,
  keywords      = "RNN;RNN To read",
  archivePrefix = "arXiv",
  eprint        = "2004.08013",
  primaryClass  = "cs.CL",
  arxivid       = "2004.08013"
}

@ARTICLE{Madhav2020-qs,
  title     = "The Synergy Between Neuroscience and Control Theory: The Nervous
               System as Inspiration for Hard Control Challenges",
  author    = "Madhav, Manu S and Cowan, Noah J",
  abstract  = "Here, we review the role of control theory in modeling neural
               control systems through a top-down analysis approach.
               Specifically, we examine the role of the brain and central
               nervous system as the controller in the organism, connected to
               but isolated from the rest of the animal through insulated
               interfaces. Though biological and engineering control systems
               operate on similar principles, they differ in several critical
               features, which makes drawing inspiration from biology for
               engineering controllers challenging but worthwhile. We also
               outline a procedure that the control theorist can use to draw
               inspiration from the biological controller: starting from the
               intact, behaving animal; designing experiments to deconstruct
               and model hierarchies of feedback; modifying feedback
               topologies; perturbing inputs and plant dynamics; using the
               resultant outputs to perform system identification; and tuning
               and validating the resultant control-theoretic model using
               specially engineered robophysical models.",
  journal   = "Annu. Rev. Control Robot. Auton. Syst.",
  publisher = "Annual Reviews",
  volume    =  3,
  number    =  1,
  pages     = "243--267",
  month     =  may,
  year      =  2020,
  issn      = "2573-5144",
  doi       = "10.1146/annurev-control-060117-104856"
}

@ARTICLE{Fieseler2020-ne,
  title         = "Unsupervised learning of control signals and their encodings
                   in $\textit{C. elegans}$ whole-brain recordings",
  author        = "Fieseler, Charles and Zimmer, Manuel and Nathan Kutz, J",
  abstract      = "Recent whole brain imaging experiments on $\textit\{C.
                   elegans\}$ has revealed that the neural population dynamics
                   encode motor commands and stereotyped transitions between
                   behaviors on low dimensional manifolds. Efforts to
                   characterize the dynamics on this manifold have used
                   piecewise linear models to describe the entire state space,
                   but it is unknown how a single, global dynamical model can
                   generate the observed dynamics. Here, we propose a control
                   framework to achieve such a global model of the dynamics,
                   whereby underlying linear dynamics is actuated by sparse
                   control signals. This method learns the control signals in
                   an unsupervised way from data, then uses $\textit\{ Dynamic
                   Mode Decomposition with control\}$ (DMDc) to create the
                   first global, linear dynamical system that can reconstruct
                   whole-brain imaging data. These control signals are shown to
                   be implicated in transitions between behaviors. In addition,
                   we analyze the time-delay encoding of these control signals,
                   showing that these transitions can be predicted from neurons
                   previously implicated in behavioral transitions, but also
                   additional neurons previously unidentified. Moreover, our
                   decomposition method allows one to understand the observed
                   nonlinear global dynamics instead as linear dynamics with
                   control. The proposed mathematical framework is generic and
                   can be generalized to other neurosensory systems,
                   potentially revealing transitions and their encodings in a
                   completely unsupervised way.",
  month         =  jan,
  year          =  2020,
  archivePrefix = "arXiv",
  eprint        = "2001.08346",
  primaryClass  = "q-bio.QM",
  arxivid       = "2001.08346"
}



@UNPUBLISHED{Schaeffer2020-qv,
  title    = "Reverse-engineering Recurrent Neural Network solutions to a
              hierarchical inference task for mice",
  author   = "Schaeffer, Rylan and Khona, Mikail and Meshulam, Leenoy and
              {International Brain Laboratory} and Fiete, Ila Rani",
  abstract = "We study how recurrent neural networks (RNNs) solve a
              hierarchical inference task involving two latent variables and
              disparate timescales separated by 1-2 orders of magnitude. The
              task is of interest to the International Brain Laboratory, a
              global collaboration of experimental and theoretical
              neuroscientists studying how the mammalian brain generates
              behavior. We make four discoveries. First, RNNs learn behavior
              that is quantitatively similar to ideal Bayesian baselines.
              Second, RNNs perform inference by learning a two-dimensional
              subspace defining beliefs about the latent variables. Third, the
              geometry of RNN dynamics reflects an induced coupling between the
              two separate inference processes necessary to solve the task.
              Fourth, we perform model compression through a novel form of
              knowledge distillation on hidden representations --
              Representations and Dynamics Distillation (RADD)-- to reduce the
              RNN dynamics to a low-dimensional, highly interpretable model.
              This technique promises a useful tool for interpretability of
              high dimensional nonlinear dynamical systems. Altogether, this
              work yields predictions to guide exploration and analysis of
              mouse neural data and circuity. \#\#\# Competing Interest
              Statement The authors have declared no competing interest.",
  journal  = "Cold Spring Harbor Laboratory",
  pages    = "2020.06.09.142745",
  month    =  jun,
  year     =  2020,
  keywords = "RNN",
  language = "en",
  doi      = "10.1101/2020.06.09.142745"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@UNPUBLISHED{Van_der_Zouwen2020-zn,
  title    = "Freely behaving mice can brake and turn during optogenetic
              stimulation of the Mesencephalic Locomotor Region",
  author   = "van der Zouwen, Cornelis Immanuel and Boutin, Jo{\"e}l and
              Foug{\`e}re, Maxime and Flaive, Aur{\'e}lie and Vivancos,
              M{\'e}lanie and Santuz, Alessandro and Akay, Turgay and Sarret,
              Philippe and Ryczko, Dimitri",
  abstract = "Background Stimulation of the Mesencephalic Locomotor Region (
              MLR ) is increasingly considered as a target to improve locomotor
              function in Parkinson's disease, spinal cord injury and stroke. A
              key function of the MLR is to control the speed of forward
              symmetrical locomotor movements. However, the ability of freely
              moving mammals to integrate environmental cues to brake and turn
              during MLR stimulation is poorly documented. Objective/hypothesis
              We investigated whether freely behaving mice could brake or turn
              based on environmental cues during MLR stimulation. Methods We
              stimulated the cuneiform nucleus in mice expressing
              channelrhodopsin in Vglut2-positive neurons in a Cre-dependent
              manner (Vglut2-ChR2-EYFP) using optogenetics. We detected
              locomotor movements using deep learning. We used patch-clamp
              recordings to validate the functional expression of
              channelrhodopsin and neuroanatomy to visualize the stimulation
              sites. Results Optogenetic stimulation of the MLR evoked
              locomotion and increasing laser power increased locomotor speed.
              Gait diagram and limb kinematics were similar during spontaneous
              and optogenetic-evoked locomotion. Mice could brake and make
              sharp turns (∼90⁰) when approaching a corner during MLR
              stimulation in an open-field arena. The speed during the turn was
              scaled with the speed before the turn, and with the turn angle.
              In a reporter mouse, many Vglut2-ZsGreen neurons were
              immunopositive for glutamate in the MLR. Patch-clamp recordings
              in Vglut2-ChR2-EYFP mice show that blue light evoked short
              latency spiking in MLR neurons. Conclusion MLR glutamatergic
              neurons are a relevant target to improve locomotor activity
              without impeding the ability to brake and turn when approaching
              an obstacle, thus ensuring smooth and adaptable navigation.
              Highlights \#\#\# Competing Interest Statement The authors have
              declared no competing interest.",
  journal  = "Cold Spring Harbor Laboratory",
  pages    = "2020.11.30.404525",
  month    =  dec,
  year     =  2020,
  keywords = "Locomotion",
  language = "en",
  doi      = "10.1101/2020.11.30.404525"
}



@UNPUBLISHED{Michaels2020-ut,
  title    = "A modular neural network model of grasp movement generation",
  author   = "Michaels, Jonathan A and Schaffelhofer, Stefan and Agudelo-Toro,
              Andres and Scherberger, Hansj{\"o}rg",
  abstract = "Summary One of the primary ways we interact with the world is
              using our hands. In macaques, the circuit spanning the anterior
              intraparietal area, the hand area of the ventral premotor cortex,
              and the primary motor cortex is necessary for transforming visual
              information into grasping movements. We hypothesized that a
              recurrent neural network mimicking the multi-area structure of
              the anatomical circuit and using visual features to generate the
              required muscle dynamics to grasp objects would explain the
              neural and computational basis of the grasping circuit. Modular
              networks with object feature input and sparse inter-module
              connectivity outperformed other models at explaining neural data
              and the inter-area relationships present in the biological
              circuit, despite the absence of neural data during network
              training. Network dynamics were governed by simple rules, and
              targeted lesioning of modules produced deficits similar to those
              observed in lesion studies, providing a potential explanation for
              how grasping movements are generated.",
  journal  = "Cold Spring Harbor Laboratory",
  pages    = "742189",
  month    =  feb,
  year     =  2020,
  keywords = "RNN;RNN To read;To Read",
  language = "en",
  doi      = "10.1101/742189"
}




@ARTICLE{Sussillo2015-xp,
  title    = "A neural network that finds a naturalistic solution for the
              production of muscle activity",
  author   = "Sussillo, David and Churchland, Mark M and Kaufman, Matthew T and
              Shenoy, Krishna V",
  abstract = "It remains an open question how neural responses in motor cortex
              relate to movement. We explored the hypothesis that motor cortex
              reflects dynamics appropriate for generating temporally patterned
              outgoing commands. To formalize this hypothesis, we trained
              recurrent neural networks to reproduce the muscle activity of
              reaching monkeys. Models had to infer dynamics that could
              transform simple inputs into temporally and spatially complex
              patterns of muscle activity. Analysis of trained models revealed
              that the natural dynamical solution was a low-dimensional
              oscillator that generated the necessary multiphasic commands.
              This solution closely resembled, at both the single-neuron and
              population levels, what was observed in neural recordings from
              the same monkeys. Notably, data and simulations agreed only when
              models were optimized to find simple solutions. An appealing
              interpretation is that the empirically observed dynamics of motor
              cortex may reflect a simple solution to the problem of generating
              temporally patterned descending commands.",
  journal  = "Nat. Neurosci.",
  volume   =  18,
  number   =  7,
  pages    = "1025--1033",
  month    =  jul,
  year     =  2015,
  keywords = "RNN;RNN To read",
  language = "en",
  issn     = "1097-6256, 1546-1726",
  pmid     = "26075643",
  doi      = "10.1038/nn.4042",
  pmc      = "PMC5113297"
}



@ARTICLE{Carlsson2020-lg,
  title     = "Topological methods for data modelling",
  author    = "Carlsson, Gunnar",
  abstract  = "The analysis of large and complex data sets is one of the most
               important problems facing the scientific community, and physics
               in particular. One response to this challenge has been the
               development of topological data analysis (TDA), which models
               data by graphs or networks rather than by linear algebraic
               (matrix) methods or cluster analysis. TDA represents the shape
               of the data (suitably defined) in a combinatorial fashion.
               Methods for measuring shape have been developed within
               mathematics, providing a toolkit referred to as homology. In
               working with data, one can use this kind of modelling to obtain
               an understanding of the overall structure of the data set. There
               is a suite of methods for constructing vector representations of
               various kinds of unstructured data. In this Review, we sketch
               the basics of TDA and provide examples where this kind of
               analysis has been carried out. The rapidly developing field of
               topological data analysis represents data via graphs rather than
               as solutions to equations or as decompositions into clusters.
               This Review discusses the methods and provides examples from
               physics and other sciences.",
  journal   = "Nature Reviews Physics",
  publisher = "Nature Publishing Group",
  pages     = "1--12",
  month     =  nov,
  year      =  2020,
  keywords  = "RNN",
  language  = "en",
  issn      = "2522-5820, 2522-5820",
  doi       = "10.1038/s42254-020-00249-3"
}

@UNPUBLISHED{Kalidindi2020-wd,
  title    = "Rotational dynamics in motor cortex are consistent with a
              feedback controller",
  author   = "Kalidindi, Hari Teja and Cross, Kevin P and Lillicrap, Timothy P
              and Omrani, Mohsen and Falotico, Egidio and Sabes, Philip N and
              Scott, Stephen H",
  abstract = "Recent studies hypothesize that motor cortical (MC) dynamics are
              generated largely through its recurrent connections based on
              observations that MC activity exhibits rotational structure.
              However, behavioural and neurophysiological studies suggest that
              MC behaves like a feedback controller where continuous sensory
              feedback and interactions with other brain areas contribute
              substantially to MC processing. We investigated these apparently
              conflicting theories by building recurrent neural networks that
              controlled a model arm and received sensory feedback about the
              limb. Networks were trained to counteract perturbations to the
              limb and to reach towards spatial targets. Network activities and
              sensory feedback signals to the network exhibited rotational
              structure even when the recurrent connections were removed.
              Furthermore, neural recordings in monkeys performing similar
              tasks also exhibited rotational structure not only in MC but also
              in somatosensory cortex. Our results argue that rotational
              structure may reflect dynamics throughout voluntary motor
              circuits involved in online control of motor actions. \#\#\#
              Competing Interest Statement SHS is co-founder and CSO of Kinarm
              which commercializes the robotic technology used in the present
              study.",
  journal  = "Cold Spring Harbor Laboratory",
  pages    = "2020.11.17.387043",
  month    =  nov,
  year     =  2020,
  keywords = "RNN",
  language = "en",
  doi      = "10.1101/2020.11.17.387043"
}


@ARTICLE{Machado2015-ig,
  title    = "A quantitative framework for whole-body coordination reveals
              specific deficits in freely walking ataxic mice",
  author   = "Machado, Ana S and Darmohray, Dana M and Fayad, Jo{\~a}o and
              Marques, Hugo G and Carey, Megan R",
  abstract = "The coordination of movement across the body is a fundamental,
              yet poorly understood aspect of motor control. Mutant mice with
              cerebellar circuit defects exhibit characteristic impairments in
              locomotor coordination; however, the fundamental features of this
              gait ataxia have not been effectively isolated. Here we describe
              a novel system (LocoMouse) for analyzing limb, head, and tail
              kinematics of freely walking mice. Analysis of visibly ataxic
              Purkinje cell degeneration (pcd) mice reveals that while
              differences in the forward motion of individual paws are fully
              accounted for by changes in walking speed and body size, more
              complex 3D trajectories and, especially, inter-limb and
              whole-body coordination are specifically impaired. Moreover, the
              coordination deficits in pcd are consistent with a failure to
              predict and compensate for the consequences of movement across
              the body. These results isolate specific impairments in
              whole-body coordination in mice and provide a quantitative
              framework for understanding cerebellar contributions to
              coordinated locomotion.",
  journal  = "Elife",
  volume   =  4,
  month    =  oct,
  year     =  2015,
  keywords = "Purkinje cell; ataxia; cerebellum; locomotion; mouse;
              neuroscience;Locomotion",
  language = "en",
  issn     = "2050-084X",
  pmid     = "26433022",
  doi      = "10.7554/eLife.07892",
  pmc      = "PMC4630674"
}

@ARTICLE{Russo2018-me,
  title    = "Motor Cortex Embeds Muscle-like Commands in an Untangled
              Population Response",
  author   = "Russo, Abigail A and Bittner, Sean R and Perkins, Sean M and
              Seely, Jeffrey S and London, Brian M and Lara, Antonio H and
              Miri, Andrew and Marshall, Najja J and Kohn, Adam and Jessell,
              Thomas M and Abbott, Laurence F and Cunningham, John P and
              Churchland, Mark M",
  abstract = "Primate motor cortex projects to spinal interneurons and
              motoneurons, suggesting that motor cortex activity may be
              dominated by muscle-like commands. Observations during reaching
              lend support to this view, but evidence remains ambiguous and
              much debated. To provide a different perspective, we employed a
              novel behavioral paradigm that facilitates comparison between
              time-evolving neural and muscle activity. We found that single
              motor cortex neurons displayed many muscle-like properties, but
              the structure of population activity was not muscle-like. Unlike
              muscle activity, neural activity was structured to avoid
              ``tangling'': moments where similar activity patterns led to
              dissimilar future patterns. Avoidance of tangling was present
              across tasks and species. Network models revealed a potential
              reason for this consistent feature: low tangling confers noise
              robustness. Finally, we were able to predict motor cortex
              activity from muscle activity by leveraging the hypothesis that
              muscle-like commands are embedded in additional structure that
              yields low tangling.",
  journal  = "Neuron",
  volume   =  97,
  number   =  4,
  pages    = "953--966.e8",
  month    =  feb,
  year     =  2018,
  keywords = "motor control; motor cortex; movement generation; neural
              dynamics; neural network; pattern generation; rhythmic
              movement;RNN;RNN To read",
  language = "en",
  issn     = "0896-6273, 1097-4199",
  pmid     = "29398358",
  doi      = "10.1016/j.neuron.2018.01.004",
  pmc      = "PMC5823788"
}

@UNPUBLISHED{Russo2019-sw,
  title    = "Neural trajectories in the supplementary motor area and primary
              motor cortex exhibit distinct geometries, compatible with
              different classes of computation",
  author   = "Russo, Abigail A and Khajeh, Ramin and Bittner, Sean R and
              Perkins, Sean M and Cunningham, John P and Abbott, Laurence F and
              Churchland, Mark M",
  abstract = "Abstract The supplementary motor area (SMA) is believed to
              contribute to higher-order aspects of motor control. To examine
              this contribution, we employed a novel cycling task and leveraged
              an emerging strategy: testing whether population trajectories
              possess properties necessary for a hypothesized class of
              computations. We found that, at the single-neuron level, SMA
              exhibited multiple response features absent in M1. We
              hypothesized that these diverse features might contribute, at the
              population level, to avoidance of `population trajectory
              divergence' -- ensuring that two trajectories never followed the
              same path before separating. Trajectory divergence was indeed
              avoided in SMA but not in M1. Network simulations confirmed that
              low trajectory divergence is necessary when guidance of future
              action depends upon internally tracking contextual factors.
              Furthermore, the empirical trajectory geometry -- helical in SMA
              versus elliptical in M1 -- was naturally reproduced by networks
              that did, versus did not, internally track context.",
  journal  = "Cold Spring Harbor Laboratory",
  pages    = "650002",
  month    =  may,
  year     =  2019,
  keywords = "RNN;RNN To read",
  language = "en",
  doi      = "10.1101/650002"
}



@ARTICLE{Rivkind2017-pf,
  title    = "Local Dynamics in Trained Recurrent Neural Networks",
  author   = "Rivkind, Alexander and Barak, Omri",
  abstract = "Learning a task induces connectivity changes in neural circuits,
              thereby changing their dynamics. To elucidate task-related neural
              dynamics, we study trained recurrent neural networks. We develop
              a mean field theory for reservoir computing networks trained to
              have multiple fixed point attractors. Our main result is that the
              dynamics of the network's output in the vicinity of attractors is
              governed by a low-order linear ordinary differential equation.
              The stability of the resulting equation can be assessed,
              predicting training success or failure. As a consequence,
              networks of rectified linear units and of sigmoidal
              nonlinearities are shown to have diametrically different
              properties when it comes to learning attractors. Furthermore, a
              characteristic time constant, which remains finite at the edge of
              chaos, offers an explanation of the network's output robustness
              in the presence of variability of the internal neural dynamics.
              Finally, the proposed theory predicts state-dependent frequency
              selectivity in the network response.",
  journal  = "Phys. Rev. Lett.",
  volume   =  118,
  number   =  25,
  pages    = "258101",
  month    =  jun,
  year     =  2017,
  keywords = "RNN",
  language = "en",
  issn     = "0031-9007, 1079-7114",
  pmid     = "28696758",
  doi      = "10.1103/PhysRevLett.118.258101"
}

@ARTICLE{Sussillo2016-zn,
  title         = "{LFADS} - Latent Factor Analysis via Dynamical Systems",
  author        = "Sussillo, David and Jozefowicz, Rafal and Abbott, L F and
                   Pandarinath, Chethan",
  abstract      = "Neuroscience is experiencing a data revolution in which many
                   hundreds or thousands of neurons are recorded
                   simultaneously. Currently, there is little consensus on how
                   such data should be analyzed. Here we introduce LFADS
                   (Latent Factor Analysis via Dynamical Systems), a method to
                   infer latent dynamics from simultaneously recorded,
                   single-trial, high-dimensional neural spiking data. LFADS is
                   a sequential model based on a variational auto-encoder. By
                   making a dynamical systems hypothesis regarding the
                   generation of the observed data, LFADS reduces observed
                   spiking to a set of low-dimensional temporal factors,
                   per-trial initial conditions, and inferred inputs. We
                   compare LFADS to existing methods on synthetic data and show
                   that it significantly out-performs them in inferring neural
                   firing rates and latent dynamics.",
  month         =  aug,
  year          =  2016,
  keywords      = "RNN To read;RNN",
  archivePrefix = "arXiv",
  eprint        = "1608.06315",
  primaryClass  = "cs.LG",
  arxivid       = "1608.06315"
}




@ARTICLE{Maheswaranathan2019-ue,
  title     = "Reverse engineering recurrent networks for sentiment
               classification reveals line attractor dynamics",
  author    = "Maheswaranathan, Niru and Williams, Alex H and Golub, Matthew D
               and Ganguli, Surya and Sussillo, David",
  abstract  = "Recurrent neural networks (RNNs) are a widely used tool for
               modeling sequential data, yet they are often treated as
               inscrutable black boxes. Given a trained recurrent network, we
               would like to reverse engineer it-to obtain a quantitative,
               interpretable description of how it solves a particular task.
               Even for simple tasks, a detailed understanding of how recurrent
               networks work, or a prescription for how to develop such an
               understanding, remains elusive. In this work, we use tools from
               dynamical systems analysis to reverse engineer recurrent
               networks trained to perform sentiment classification, a
               foundational natural language processing task. Given a trained
               network, we find fixed points of the recurrent dynamics and
               linearize the nonlinear system around these fixed points.
               Despite their theoretical capacity to implement complex,
               high-dimensional computations, we find that trained networks
               converge to highly interpretable, low-dimensional
               representations. In particular, the topological structure of the
               fixed points and corresponding linearized dynamics reveal an
               approximate line attractor within the RNN, which we can use to
               quantitatively understand how the RNN solves the sentiment
               analysis task. Finally, we find this mechanism present across
               RNN architectures (including LSTMs, GRUs, and vanilla RNNs)
               trained on multiple datasets, suggesting that our findings are
               not unique to a particular architecture or dataset. Overall,
               these results demonstrate that surprisingly universal and human
               interpretable computations can arise across a range of recurrent
               networks.",
  journal   = "Adv. Neural Inf. Process. Syst.",
  publisher = "papers.nips.cc",
  volume    =  32,
  pages     = "15696--15705",
  month     =  dec,
  year      =  2019,
  keywords  = "RNN To read;RNN",
  language  = "en",
  issn      = "1049-5258",
  pmid      = "32782423",
  pmc       = "PMC7416638"
}


@ARTICLE{Maheswaranathan2019-ux,
  title    = "Universality and individuality in neural dynamics across large
              populations of recurrent networks",
  author   = "Maheswaranathan, Niru and Williams, Alex H and Golub, Matthew D
              and Ganguli, Surya and Sussillo, David",
  abstract = "Task-based modeling with recurrent neural networks (RNNs) has
              emerged as a popular way to infer the computational function of
              different brain regions. These models are quantitatively assessed
              by comparing the low-dimensional neural representations of the
              model with the brain, for example using canonical correlation
              analysis (CCA). However, the nature of the detailed
              neurobiological inferences one can draw from such efforts remains
              elusive. For example, to what extent does training neural
              networks to solve common tasks uniquely determine the network
              dynamics, independent of modeling architectural choices? Or
              alternatively, are the learned dynamics highly sensitive to
              different model choices? Knowing the answer to these questions
              has strong implications for whether and how we should use
              task-based RNN modeling to understand brain dynamics. To address
              these foundational questions, we study populations of thousands
              of networks, with commonly used RNN architectures, trained to
              solve neuroscientifically motivated tasks and characterize their
              nonlinear dynamics. We find the geometry of the RNN
              representations can be highly sensitive to different network
              architectures, yielding a cautionary tale for measures of
              similarity that rely on representational geometry, such as CCA.
              Moreover, we find that while the geometry of neural dynamics can
              vary greatly across architectures, the underlying computational
              scaffold-the topological structure of fixed points, transitions
              between them, limit cycles, and linearized dynamics-often appears
              universal across all architectures.",
  journal  = "Adv. Neural Inf. Process. Syst.",
  volume   =  2019,
  pages    = "15629--15641",
  month    =  dec,
  year     =  2019,
  keywords = "RNN",
  language = "en",
  issn     = "1049-5258",
  pmid     = "32782422",
  pmc      = "PMC7416639"
}

@ARTICLE{Vyas2020-pw,
  title    = "Computation Through Neural Population Dynamics",
  author   = "Vyas, Saurabh and Golub, Matthew D and Sussillo, David and
              Shenoy, Krishna V",
  abstract = "Significant experimental, computational, and theoretical work has
              identified rich structure within the coordinated activity of
              interconnected neural populations. An emerging challenge now is
              to uncover the nature of the associated computations, how they
              are implemented, and what role they play in driving behavior. We
              term this computation through neural population dynamics. If
              successful, this framework will reveal general motifs of neural
              population activity and quantitatively describe how neural
              population dynamics implement computations necessary for driving
              goal-directed behavior. Here, we start with a mathematical primer
              on dynamical systems theory and analytical tools necessary to
              apply this perspective to experimental data. Next, we highlight
              some recent discoveries resulting from successful application of
              dynamical systems. We focus on studies spanning motor control,
              timing, decision-making, and working memory. Finally, we briefly
              discuss promising recent lines of investigation and future
              directions for the computation through neural population dynamics
              framework.",
  journal  = "Annu. Rev. Neurosci.",
  volume   =  43,
  pages    = "249--275",
  month    =  jul,
  year     =  2020,
  keywords = "dynamical systems; neural computation; neural population
              dynamics; state spaces;RNN",
  language = "en",
  issn     = "0147-006X, 1545-4126",
  pmid     = "32640928",
  doi      = "10.1146/annurev-neuro-092619-094115",
  pmc      = "PMC7402639"
}

@ARTICLE{Bellardita2015-ut,
  title     = "Phenotypic characterization of speed-associated gait changes in
               mice reveals modular organization of locomotor networks",
  author    = "Bellardita, Carmelo and Kiehn, Ole",
  abstract  = "Studies of locomotion in mice suggest that circuits controlling
               the alternating between left and right limbs may have a modular
               organization with distinct locomotor circuits being recruited at
               different speeds. It is not clear, however, whether such a
               modular organization reflects specific behavioral outcomes
               expressed at different speeds of locomotion. Here, we use
               detailed kinematic analyses to search for signatures of a
               modular organization of locomotor circuits in intact and
               genetically modified mice moving at different speeds of
               locomotion. We show that wild-type mice display three distinct
               gaits: two alternating, walk and trot, and one synchronous,
               bound. Each gait is expressed in distinct ranges of speed with
               phenotypic inter-limb and intra-limb coordination. A fourth
               gait, gallop, closely resembled bound in most of the locomotor
               parameters but expressed diverse inter-limb coordination.
               Genetic ablation of commissural V0V neurons completely removed
               the expression of one alternating gait, trot, but left intact
               walk, gallop, and bound. Ablation of commissural V0V and V0D
               neurons led to a loss of walk, trot, and gallop, leaving bound
               as the default gait. Our study provides a benchmark for studies
               of the neuronal control of locomotion in the full range of
               speeds. It provides evidence that gait expression depends upon
               selection of different modules of neuronal ensembles.",
  journal   = "Curr. Biol.",
  publisher = "Elsevier",
  volume    =  25,
  number    =  11,
  pages     = "1426--1436",
  month     =  jun,
  year      =  2015,
  keywords  = "Locomotion",
  language  = "en",
  issn      = "0960-9822, 1879-0445",
  pmid      = "25959968",
  doi       = "10.1016/j.cub.2015.04.005",
  pmc       = "PMC4469368"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Walker2018-qp,
  title    = "A comparison of two types of running wheel in terms of mouse
              preference, health, and welfare",
  author   = "Walker, Michael and Mason, Georgia",
  abstract = "Voluntary wheel running occurs in mice of all strains, sexes, and
              ages. Mice find voluntary wheel running rewarding, and it leads
              to numerous health benefits. For this reason wheels are used both
              to enhance welfare and to create models of exercise. However,
              many designs of running wheel are used. This makes between-study
              comparisons difficult, as this variability could potentially
              affect the amount, pattern, and/or intensity of running
              behaviour, and thence the wheels' effects on welfare and
              exercise-related changes in anatomy and physiology. This study
              therefore evaluated two commercially available models, chosen
              because safe for group-housed mice: Bio Serv\textregistered{}'s
              ``fast-trac'' wheel combo and Ware Manufacturing Inc.'s stainless
              steel mesh 5″ upright wheel. Working with a total of three
              hundred and fifty one female C57BL/6, DBA/2 and BALB/c mice, we
              assessed these wheels' relative utilization by mice when access
              was free; the strength of motivation for each wheel-type when
              access required crossing an electrified grid; and the impact each
              wheel had on mouse well-being (inferred from acoustic startle
              responses and neophobia) and exercise-related anatomical changes
              (BMI; heart and hind limb masses). Mice ran more on the
              ``fast-trac'' wheel regardless of whether both wheel-types were
              available at once, or only if one was present. In terms of
              motivation, subjects required to work to access a single wheel
              worked equally hard for both wheel-types (even if locked and thus
              not useable for running), but if provided with one working wheel
              for free and the other type of wheel (again unlocked) accessible
              via crossing the electrified grid, the ``fast-trac'' wheel
              emerged as more motivating, as the Maximum Price Paid for the
              Ware metal wheel was lower than that paid for the ``fast-trac''
              plastic wheel, at least for C57BL/6s and DBA/2s. No deleterious
              consequences were noted with either wheel in terms of health and
              welfare, but only mice with plastic wheels developed
              significantly larger hearts and hind limbs than control animals
              with locked wheels. Thus, where differences emerged, Bio
              Serv\textregistered{}'s ``fast-trac'' wheel combos appeared to
              better meet the aims of exercise provision than Ware
              Manufacturing's steel upright wheels.",
  journal  = "Physiol. Behav.",
  volume   =  191,
  pages    = "82--90",
  month    =  jul,
  year     =  2018,
  keywords = "Health; Motivation; Mouse; Preference; Welfare; Wheel running",
  language = "en",
  issn     = "0031-9384, 1873-507X",
  pmid     = "29653112",
  doi      = "10.1016/j.physbeh.2018.04.006"
}

@ARTICLE{Lemieux2016-fx,
  title    = "{Speed-Dependent} Modulation of the Locomotor Behavior in Adult
              Mice Reveals Attractor and Transitional Gaits",
  author   = "Lemieux, Maxime and Josset, Nicolas and Roussel, Marie and
              Couraud, S{\'e}bastien and Bretzner, Fr{\'e}d{\'e}ric",
  abstract = "Locomotion results from an interplay between biomechanical
              constraints of the muscles attached to the skeleton and the
              neuronal circuits controlling and coordinating muscle activities.
              Quadrupeds exhibit a wide range of locomotor gaits. Given our
              advances in the genetic identification of spinal and supraspinal
              circuits important to locomotion in the mouse, it is now
              important to get a better understanding of the full repertoire of
              gaits in the freely walking mouse. To assess this range, young
              adult C57BL/6J mice were trained to walk and run on a treadmill
              at different locomotor speeds. Instead of using the classical
              paradigm defining gaits according to their footfall pattern, we
              combined the inter-limb coupling and the duty cycle of the stance
              phase, thus identifying several types of gaits: lateral walk,
              trot, out-of-phase walk, rotary gallop, transverse gallop, hop,
              half-bound, and full-bound. Out-of-phase walk, trot, and
              full-bound were robust and appeared to function as attractor
              gaits (i.e., a state to which the network flows and stabilizes)
              at low, intermediate, and high speeds respectively. In contrast,
              lateral walk, hop, transverse gallop, rotary gallop, and
              half-bound were more transient and therefore considered
              transitional gaits (i.e., a labile state of the network from
              which it flows to the attractor state). Surprisingly, lateral
              walk was less frequently observed. Using graph analysis, we
              demonstrated that transitions between gaits were predictable, not
              random. In summary, the wild-type mouse exhibits a wider
              repertoire of locomotor gaits than expected. Future locomotor
              studies should benefit from this paradigm in assessing transgenic
              mice or wild-type mice with neurotraumatic injury or
              neurodegenerative disease affecting gait.",
  journal  = "Front. Neurosci.",
  volume   =  10,
  pages    = "42",
  month    =  feb,
  year     =  2016,
  keywords = "graph analysis; kinematic; locomotor gaits; mouse; speed;
              steady-state;Locomotion",
  language = "en",
  issn     = "1662-4548, 1662-453X",
  pmid     = "26941592",
  doi      = "10.3389/fnins.2016.00042",
  pmc      = "PMC4763020"
}

@ARTICLE{Herbin2006-mc,
  title    = "How does a mouse increase its velocity? A model for investigation
              in the control of locomotion",
  author   = "Herbin, Marc and Gasc, Jean-Pierre and Renous, Sabine",
  abstract = "We analysed treadmill locomotion of the adult SWISS-OF1 mice over
              a large range of velocities. The use of a high-speed video camera
              combined with cinefluoroscopic equipment allowed us to quantify
              in detail the various space and time parameters of limb
              kinematics. We find that velocity adjustments depend upon whether
              animal used a symmetrical or non-symmetrical gait. In symmetrical
              gaits, the increase of velocity generally results equally from an
              increase in the stride frequency and the stride length. On the
              other hand, in non-symmetrical gaits, the increase in velocity is
              achieved differently according to the level of velocity used. As
              speed increases, velocity increases first as a consequence of
              increased stride frequency, then as in symmetrical gaits, by an
              equal increase in both variables, and finally at high speed,
              velocity increases through increased stride length. In both
              symmetrical and non-symmetrical gaits, stance and swing-time
              shortening contributed to the increase of the stride frequency,
              with stance time decrease being the major contributor. The
              pattern of locomotion obtained in the present study may be used
              as a model mouse system for studying locomotor deficits resulting
              from specific mutations in the nervous system. To cite this
              article: M. Herbin et al., C. R. Palevol 5 (2006). R{\'e}sum{\'e}
              Comment la souris augmente-elle sa vitesse ? Un mod{\`e}le pour
              la recherche sur le contr{\^o}le moteur de la locomotion. La
              locomotion sur tapis roulant de la souche de souris SWISS-OF1 a
              {\'e}t{\'e} analys{\'e}e {\`a} travers une large gamme de
              vitesses. L'utilisation de la vid{\'e}oradiographie {\`a} grande
              vitesse a permis de quantifier de fa{\c c}on tr{\`e}s
              d{\'e}taill{\'e}e tous les param{\`e}tres de la cin{\'e}matique
              du membre de r{\'e}f{\'e}rence. Les r{\'e}sultats ainsi obtenus
              montrent que la fr{\'e}quence et l'enjamb{\'e}e n'interviennent
              pas de la m{\^e}me fa{\c c}on dans l'augmentation de la vitesse,
              selon l'allure utilis{\'e}e. Lorsque l'animal est en allure
              sym{\'e}trique, l'augmentation de la vitesse est
              g{\'e}n{\'e}ralement obtenue par une {\'e}gale augmentation de la
              fr{\'e}quence et de l'enjamb{\'e}e. En revanche, si la souris
              utilise une allure non sym{\'e}trique, l'augmentation de la
              vitesse est obtenue diff{\'e}remment selon la valeur de cette
              derni{\`e}re. L'augmentation de la vitesse est d'abord surtout
              assur{\'e}e par une augmentation de la fr{\'e}quence, puis par
              l'augmentation {\'e}gale des deux variables et enfin surtout par
              l'augmentation de l'enjamb{\'e}e. L'augmentation de la
              fr{\'e}quence est, en revanche, surtout assur{\'e}e par une
              diminution de la dur{\'e}e du pos{\'e} et cela, quelle que soit
              l'allure utilis{\'e}e. Cette mod{\'e}lisation de la locomotion
              normale de la souris pourra {\^e}tre utilis{\'e}e comme
              r{\'e}f{\'e}rentiel pour les {\'e}tudes portant sur les
              d{\'e}ficits moteurs de certaines souches de souris mutantes ou
              transg{\'e}niques. Pour citer cet article : M. Herbin et al., C.
              R. Palevol 5 (2006).",
  journal  = "C. R. Palevol",
  volume   =  5,
  number   =  3,
  pages    = "531--540",
  month    =  mar,
  year     =  2006,
  keywords = "Stride frequency; Stride length; Treadmill; Locomotion;
              SWISS-OF1; Fr{\'e}quence; Enjamb{\'e}e; Tapis roulant;
              Locomotion; SWISS-OF1;Locomotion",
  issn     = "1631-0683",
  doi      = "10.1016/j.crpv.2005.12.012"
}

@ARTICLE{Walter2003-pb,
  title    = "Kinematics of 90 degrees running turns in wild mice",
  author   = "Walter, Rebecca M",
  abstract = "Turning is a requirement for locomotion on the variable terrain
              that most terrestrial animals inhabit and is a deciding factor in
              many predator-prey interactions. Despite this, the kinematics and
              mechanics of quadrupedal turns are not well understood. To gain
              insight to the turning kinematics of small quadrupedal mammals,
              six adult wild mice were videotaped at 250 Hz from below as they
              performed 90 degrees running turns. Four markers placed along the
              sagittal axis were digitized to allow observation of lateral
              bending and body rotation throughout the turn. Ground contact
              periods of the fore- and hindlimbs were also noted for each
              frame. During turning, mice increased their ground contact time,
              but did not change their stride frequency relative to straight
              running at maximum speed. Postcranial body rotation preceded
              deflection in heading, and did not occur in one continuous
              motion, but rather in bouts of 15-53 degrees. These bouts were
              synchronized with the stride cycle, such that the majority of
              rotation occurred during the second half of forelimb support and
              the first half of hindlimb support. In this phase of the stride
              cycle, the trunk was sagittally flexed and rotational inertia was
              65\% of that during maximal extension. By synchronizing body
              rotation with this portion of the stride cycle, mice can achieve
              a given angular acceleration with much lower applied torque.
              Compared with humans running along curved trajectories, mice
              maintained relatively higher speeds at proportionately smaller
              radii. A possible explanation for this difference lies in the
              more crouched limb posture of mice, which increases the
              mechanical advantage for horizontal ground force production. The
              occurrence of body rotation prior to deflection in heading may
              facilitate acceleration in the new direction by making use of the
              relatively greater force production inherent in the parasagittal
              limb posture of mice.",
  journal  = "J. Exp. Biol.",
  volume   =  206,
  number   = "Pt 10",
  pages    = "1739--1749",
  month    =  may,
  year     =  2003,
  language = "en",
  issn     = "0022-0949",
  pmid     = "12682105",
  doi      = "10.1242/jeb.00349"
}

@ARTICLE{Herbin2004-ma,
  title    = "Symmetrical and asymmetrical gaits in the mouse: patterns to
              increase velocity",
  author   = "Herbin, Marc and Gasc, Jean-Pierre and Renous, Sabine",
  abstract = "The gaits of the adult SWISS mice during treadmill locomotion at
              velocities ranging from 15 to 85 cm s(-1) have been analysed
              using a high-speed video camera combined with cinefluoroscopic
              equipment. The sequences of locomotion were analysed to determine
              the various space and time parameters of limb kinematics. We
              found that velocity adjustments are accounted for differently by
              the stride frequency and the stride length if the animal showed a
              symmetrical or an asymmetrical gait. In symmetrical gaits, the
              increase of velocity is provided by an equal increase in the
              stride length and the stride frequency. In asymmetrical gaits,
              the increase in velocity is mainly assured by an increase in the
              stride frequency in velocities ranging from 15 to 29 cm s(-1).
              Above 68 cm s(-1), velocity increase is achieved by stride length
              increase. In velocities ranging from 29 to 68 cm s(-1), the
              contribution of both variables is equal as in symmetrical gaits.
              Both stance time and swing time shortening contributed to the
              increase of the stride frequency in both gaits, though with a
              major contribution from stance time decrease. The pattern of
              locomotion obtained in a normal mouse should be used as a
              template for studying locomotor control deficits after lesions or
              in different mutations affecting the nervous system.",
  journal  = "J. Comp. Physiol. A Neuroethol. Sens. Neural Behav. Physiol.",
  volume   =  190,
  number   =  11,
  pages    = "895--906",
  month    =  nov,
  year     =  2004,
  keywords = "Locomotion",
  language = "en",
  issn     = "0340-7594",
  pmid     = "15449091",
  doi      = "10.1007/s00359-004-0545-0"
}

@ARTICLE{Josset2018-js,
  title    = "Distinct Contributions of Mesencephalic Locomotor Region Nuclei
              to Locomotor Control in the Freely Behaving Mouse",
  author   = "Josset, Nicolas and Roussel, Marie and Lemieux, Maxime and
              Lafrance-Zoubga, David and Rastqar, Ali and Bretzner, Frederic",
  abstract = "The mesencephalic locomotor region (MLR) has been initially
              identified as a supraspinal center capable of initiating and
              modulating locomotion. Whereas its functional contribution to
              locomotion has been widely documented throughout the phylogeny
              from the lamprey to humans, there is still debate about its exact
              organization. Combining kinematic and electrophysiological
              recordings in mouse genetics, our study reveals that
              glutamatergic neurons of the cuneiform nucleus initiate
              locomotion and induce running gaits, whereas glutamatergic and
              cholinergic neurons of the pedunculopontine nucleus modulate
              locomotor pattern and rhythm, contributing to slow-walking gaits.
              By initiating, modulating, and accelerating locomotion, our study
              identifies and characterizes distinct neuronal populations of
              this functional region important to locomotor command.",
  journal  = "Curr. Biol.",
  volume   =  28,
  number   =  6,
  pages    = "884--901.e3",
  month    =  mar,
  year     =  2018,
  keywords = "cuneiform nucleus; electrophysiology; glutamatergic and
              cholinergic neurons; kinematic analysis; locomotor command;
              locomotor pattern rhythm and gait; mesencephalic locomotor
              region; optogenetic tools; pedunculopontine nucleus;Locomotion",
  language = "en",
  issn     = "0960-9822, 1879-0445",
  pmid     = "29526593",
  doi      = "10.1016/j.cub.2018.02.007"
}

@ARTICLE{Herbin2007-us,
  title    = "Gait parameters of treadmill versus overground locomotion in
              mouse",
  author   = "Herbin, Marc and Hackert, R{\'e}mi and Gasc, Jean-Pierre and
              Renous, Sabine",
  abstract = "Many studies of interest in motor behaviour and motor impairment
              in mice use equally treadmill or track as a routine test.
              However, the literature in mammals shows a wide difference of
              results between the kinematics of treadmill and overground
              locomotion. To study these discrepancies, we analyzed the
              locomotion of adult SWISS-OF1 mice over a large range of
              velocities using treadmill and overground track. The use of a
              high-speed video camera combined with cinefluoroscopic equipment
              allowed us to quantify in detail the various space and time
              parameters of limb kinematics. The results show that mice
              maintain the same gait pattern in both conditions. However, they
              also demonstrate that during treadmill exercise mice always
              exhibit higher stride frequency and consequently lower stride
              length. The relationship of the stance time and the swing time
              against the stride frequency are still the same in both
              conditions. We conclude that the conflict related to the
              discrepancy between the proprioceptive, vestibular, and visual
              inputs contribute to an increase in the stride frequency during
              the treadmill locomotion.",
  journal  = "Behav. Brain Res.",
  volume   =  181,
  number   =  2,
  pages    = "173--179",
  month    =  aug,
  year     =  2007,
  keywords = "Locomotion",
  language = "en",
  issn     = "0166-4328",
  pmid     = "17521749",
  doi      = "10.1016/j.bbr.2007.04.001"
}


% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Fiker2020-kd,
  title    = "Visual Gait Lab: A user-friendly approach to gait analysis",
  author   = "Fiker, Robert and Kim, Linda H and Molina, Leonardo A and
              Chomiak, Taylor and Whelan, Patrick J",
  abstract = "BACKGROUND: Gait analysis forms a critical part of many lab
              workflows, ranging from those interested in preclinical
              neurological models to others who use locomotion as part of a
              standard battery of tests. Unfortunately, while paw detection can
              be semi-automated, it becomes generally a time-consuming process
              with error corrections. Improvement in paw tracking would aid in
              better gait analysis performance and experience. NEW METHOD: Here
              we show the use of Visual Gait Lab (VGL), a high-level software
              with an intuitive, easy to use interface, that is built on
              DeepLabCut™. VGL is optimized to generate gait metrics and allows
              for quick manual error corrections. VGL comes with a single
              executable, streamlining setup on Windows systems. We demonstrate
              the use of VGL to analyze gait. RESULTS: Training and evaluation
              of VGL were conducted using 200 frames (80/20 train-test split)
              of video from mice walking on a treadmill. The trained network
              was then used to visually track paw placements to compute gait
              metrics. These are processed and presented on the screen where
              the user can rapidly identify and correct errors. COMPARISON WITH
              EXISTING METHODS: Gait analysis remains cumbersome, even with
              commercial software due to paw detection errors. DeepLabCut™ is
              an alternative that can improve visual tracking but is not
              optimized for gait analysis functionality. CONCLUSIONS: VGL
              allows for gait analysis to be performed in a rapid, unbiased
              manner, with a set-up that can be easily implemented and executed
              by those without a background in computer programming.",
  journal  = "J. Neurosci. Methods",
  volume   =  341,
  pages    = "108775",
  month    =  may,
  year     =  2020,
  keywords = "DeepLabCut™; Gait analysis; Gait tracking system; Motor control;
              Mouse locomotion",
  language = "en",
  issn     = "0165-0270, 1872-678X",
  pmid     = "32428621",
  doi      = "10.1016/j.jneumeth.2020.108775"
}
@MISC{Valente2007-qx,
  title    = "Analysis of the Trajectory of Drosophila melanogaster in a
              Circular Open Field Arena",
  author   = "Valente, Dan and Golani, Ilan and Mitra, Partha P",
  editor   = "Scalas, Enrico",
  abstract = "BACKGROUND Obtaining a complete phenotypic characterization of a
              freely moving organism is a difficult task, yet such a
              description is desired in many neuroethological studies. Many
              metrics currently used in the literature to describe locomotor
              and exploratory behavior are typically based on average
              quantities or subjectively chosen spatial and temporal
              thresholds. All of these measures are relatively coarse-grained
              in the time domain. It is advantageous, however, to employ
              metrics based on the entire trajectory that an organism takes
              while exploring its environment. METHODOLOGY/PRINCIPAL FINDINGS
              To characterize the locomotor behavior of Drosophila
              melanogaster, we used a video tracking system to record the
              trajectory of a single fly walking in a circular open field
              arena. The fly was tracked for two hours. Here, we present
              techniques with which to analyze the motion of the fly in this
              paradigm, and we discuss the methods of calculation. The measures
              we introduce are based on spatial and temporal probability
              distributions and utilize the entire time-series trajectory of
              the fly, thus emphasizing the dynamic nature of locomotor
              behavior. Marginal and joint probability distributions of speed,
              position, segment duration, path curvature, and reorientation
              angle are examined and related to the observed behavior.
              CONCLUSIONS/SIGNIFICANCE The measures discussed in this paper
              provide a detailed profile of the behavior of a single fly and
              highlight the interaction of the fly with the environment. Such
              measures may serve as useful tools in any behavioral study in
              which the movement of a fly is an important variable and can be
              incorporated easily into many setups, facilitating
              high-throughput phenotypic characterization.",
  month    =  oct,
  year     =  2007,
  doi      = "10.1371/journal.pone.0001083"
}


% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Barthas2017-zs,
  title     = "Secondary motor cortex: where `sensory'meets `motor'in the
               rodent frontal cortex",
  author    = "Barthas, Florent and Kwan, Alex C",
  abstract  = "In rodents, the medial aspect of the secondary motor cortex (M2)
               is known by other names, including medial agranular cortex
               (AGm), medial precentral cortex (PrCm), and frontal orienting
               field (FOF). As a subdivision of the medial prefrontal cortex
               (mPFC), M2 can be defined by a distinct set of afferent and
               efferent connections, microstimulation responses, and lesion
               outcomes. However, the behavioral role of M2 remains mysterious.
               Here, we focus on evidence from rodent studies, highlighting
               recent findings of early and context …",
  journal   = "Trends Neurosci.",
  publisher = "Elsevier",
  volume    =  40,
  number    =  3,
  pages     = "181--193",
  year      =  2017,
  keywords  = "To Read",
  issn      = "0166-2236"
}


@ARTICLE{Olson2020-lm,
  title     = "Secondary Motor Cortex Transforms Spatial Information into
               Planned Action during Navigation",
  author    = "Olson, Jacob M and Li, Jamie K and Montgomery, Sarah E and Nitz,
               Douglas A",
  abstract  = "Fluid navigation requires constant updating of planned movements
               to adapt to evolving obstacles and goals. For that reason, a
               neural substrate for navigation demands spatial and
               environmental information and the ability to effect actions
               through efferents. The secondary motor cortex (M2) is a prime
               candidate for this role given its interconnectivity with
               association cortices that encode spatial relationships and its
               projection to the primary motor cortex. Here, we report that M2
               neurons robustly encode both planned and current left/right
               turning actions across multiple turn locations in a multi-route
               navigational task. Comparisons within a common statistical
               framework reveal that M2 neurons differentiate contextual
               factors, including environmental position, route, action
               sequence, orientation, and choice availability. Despite
               significant modulation by environmental factors, action
               planning, and execution are the dominant output signals of M2
               neurons. These results identify the M2 as a structure
               integrating spatial information toward the updating of planned
               movements.",
  journal   = "Curr. Biol.",
  publisher = "Elsevier",
  volume    =  30,
  number    =  10,
  pages     = "1845--1854.e4",
  month     =  may,
  year      =  2020,
  keywords  = "M2; action; allocentric; cortical circuits; decision making;
               egocentric; in vivo electrophysiology; navigation; parietal
               cortex; retrosplenial cortex; systems neuroscience;Locomotion",
  language  = "en",
  issn      = "0960-9822, 1879-0445",
  pmid      = "32302586",
  doi       = "10.1016/j.cub.2020.03.016"
}

@ARTICLE{Jordan2008-dx,
  title     = "Descending command systems for the initiation of locomotion in
               mammals",
  author    = "Jordan, Larry M and Liu, Jun and Hedlund, Peter B and Akay,
               Turgay and Pearson, Keir G",
  abstract  = "Neurons in the brainstem implicated in the initiation of
               locomotion include glutamatergic, noradrenergic (NA),
               dopaminergic (DA), and serotonergic (5-HT) neurons giving rise
               to descending tracts. Glutamate antagonists block mesencephalic
               locomotor region-induced and spontaneous locomotion, and
               glutamatergic agonists induce locomotion in spinal animals. NA
               and 5-HT inputs to the spinal cord originate in the brainstem,
               while the descending dopaminergic pathway originates in the
               hypothalamus. Agonists acting at NA, DA or 5-HT receptors
               facilitate or induce locomotion in spinal animals. 5-HT neurons
               located in the parapyramidal region (PPR) produce locomotion
               when stimulated in the isolated neonatal rat brainstem-spinal
               cord preparation, and they constitute the first anatomically
               discrete group of spinally-projecting neurons demonstrated to be
               involved in the initiation of locomotion in mammals. Neurons in
               the PPR are activated during treadmill locomotion in adult rats.
               Locomotion evoked from the PPR is mediated by 5-HT(7) and
               5-HT(2A) receptors, and 5-HT(7) antagonists block locomotion in
               cat, rat and mouse preparations, but have little effect in mice
               lacking 5-HT(7) receptors. 5-HT induced activity in 5-HT(7)
               knockout mice is rhythmic, but coordination among flexor and
               extensor motor nuclei and left and right sides of the spinal
               cord is disrupted. In the adult wild-type mouse, 5-HT(7)
               receptor antagonists impair locomotion, producing patterns of
               activity resembling those induced by 5-HT in 5-HT(7) knockout
               mice. 5-HT(7) receptor antagonists have a reduced effect on
               locomotion in adult 5-HT(7) receptor knockout mice. We conclude
               that the PPR is the source of a descending 5-HT command pathway
               that activates the CPG via 5-HT(7) and 5-HT(2A) receptors.
               Further experiments are necessary to define the putative
               glutamatergic, DA, and NA command pathways.",
  journal   = "Brain Res. Rev.",
  publisher = "Elsevier",
  volume    =  57,
  number    =  1,
  pages     = "183--191",
  month     =  jan,
  year      =  2008,
  language  = "en",
  issn      = "0165-0173",
  pmid      = "17928060",
  doi       = "10.1016/j.brainresrev.2007.07.019"
}

@ARTICLE{Ryczko2013-pw,
  title     = "The multifunctional mesencephalic locomotor region",
  author    = "Ryczko, Dimitri and Dubuc, R{\'e}jean",
  abstract  = "In 1966, Shik, Severin and Orlovskii discovered that electrical
               stimulation of a region at the junction between the midbrain and
               hindbrain elicited controlled walking and running in the cat.
               The region was named Mesencephalic Locomotor Region (MLR). Since
               then, this locomotor center was shown to control locomotion in
               various vertebrate species, including the lamprey, salamander,
               stingray, rat, guinea-pig, rabbit or monkey. In human subjects
               asked to imagine they are walking, there is an increased
               activity in brainstem nuclei corresponding to the MLR (i.e.
               pedunculopontine, cuneiform and subcuneiform nuclei). Clinicians
               are now stimulating (deep brain stimulation) structures
               considered to be part of the MLR to alleviate locomotor symptoms
               of patients with Parkinson's disease. However, the anatomical
               constituents of the MLR still remain a matter of debate,
               especially relative to the pedunculopontine, cuneiform and
               subcuneiform nuclei. Furthermore, recent studies in lampreys
               have revealed that the MLR is more complex than a simple relay
               in a serial descending pathway activating the spinal locomotor
               circuits. It has multiple functions. Our goal is to review the
               current knowledge relative to the anatomical constituents of the
               MLR, and its physiological role, from lamprey to man. We will
               discuss these results in the context of the recent clinical
               studies involving stimulation of the MLR in patients with
               Parkinson's disease.",
  journal   = "Curr. Pharm. Des.",
  publisher = "ingentaconnect.com",
  volume    =  19,
  number    =  24,
  pages     = "4448--4470",
  year      =  2013,
  keywords  = "Locomotion",
  language  = "en",
  issn      = "1381-6128, 1873-4286",
  pmid      = "23360276",
  doi       = "10.2174/1381612811319240011"
}


@ARTICLE{Grillner2008-ev,
  title     = "Neural bases of goal-directed locomotion in vertebrates---An
               overview",
  author    = "Grillner, Sten and Wall{\'e}n, Peter and Saitoh, Kazuya and
               Kozlov, Alexander and Robertson, Brita",
  abstract  = "The different neural control systems involved in goal-directed
               vertebrate locomotion are reviewed. They include not only the
               central pattern generator networks in the spinal cord that
               generate the basic locomotor synergy and the brainstem command
               systems for locomotion but also the control systems for steering
               and control of body orientation (posture) and finally the neural
               structures responsible for determining which motor programs
               should be turned on in a given instant. The role of the basal
               ganglia is considered in this context. The review summarizes the
               available information from a general vertebrate perspective, but
               specific examples are often derived from the lamprey, which
               provides the most detailed information when considering cellular
               and network perspectives.",
  journal   = "Brain Res. Rev.",
  publisher = "Elsevier",
  volume    =  57,
  number    =  1,
  pages     = "2--12",
  month     =  jan,
  year      =  2008,
  keywords  = "Basal ganglia; Lamprey; Central pattern generator; Tectum; Brain
               stem--spinal cord; Modeling",
  issn      = "0165-0173",
  doi       = "10.1016/j.brainresrev.2007.06.027"
}

@ARTICLE{Drew2004-kl,
  title     = "Cortical and brainstem control of locomotion",
  author    = "Drew, Trevor and Prentice, Stephen and Schepens,
               B{\'e}n{\'e}dicte",
  abstract  = "While a basic locomotor rhythm is centrally generated by spinal
               circuits, descending pathways are critical for ensuring
               appropriate anticipatory modifications of gait to accommodate
               uneven terrain. Neurons in the motor cortex command the changes
               in muscle activity required to modify limb trajectory when
               stepping over obstacles. Simultaneously, neurons in the
               brainstem reticular formation ensure that these modifications
               are superimposed on an appropriate base of postural support.
               Recent experiments suggest that the same neurons in the same
               structures also provide similar information during reaching
               movements. It is suggested that, during both locomotion and
               reaching movements, the final expression of descending signals
               is influenced by the state and excitability of the spinal
               circuits upon which they impinge.",
  journal   = "Prog. Brain Res.",
  publisher = "Elsevier",
  volume    =  143,
  pages     = "251--261",
  year      =  2004,
  keywords  = "Locomotion",
  language  = "en",
  issn      = "0079-6123",
  pmid      = "14653170",
  doi       = "10.1016/S0079-6123(03)43025-2"
}

@UNPUBLISHED{Storchi2020-em,
  title    = "Beyond locomotion: in the mouse the mapping between sensations
              and behaviours unfolds in a higher dimensional space",
  author   = "Storchi, Riccardo and Milosavljevic, Nina and Allen, Annette E
              and Cootes, Timothy F and Lucas, Robert J",
  abstract = "Abstract The ability of specific sensory stimuli to evoke
              spontaneous behavioural responses in the mouse represents a
              powerful approach to study how the mammalian brain processes
              sensory information and selects appropriate motor actions. For
              visually and auditory guided behaviours the relevant action has
              been empirically identified as a change in locomotion state.
              However, the extent to which locomotion alone captures the
              diversity of those behaviours and their sensory specificity is
              unknown.To tackle this problem we developed a method to obtain a
              faithful 3D reconstruction of the mouse body that enabled us to
              quantify a wide variety of movements and changes in postures.
              This higher dimensional description of behaviour revealed that
              responses to different sensory inputs is more stimulus-specific
              than indicated by locomotion data alone. Thus, equivalent
              locomotion patterns evoked by different stimuli (e.g. looming and
              sound evoking locomotion arrest) could be well separated along
              other dimensions. The enhanced stimulus-specificity was explained
              by a surprising diversity of behavioural responses. A clustering
              analysis revealed that distinct combinations of motor actions and
              postures, giving rise to at least 7 different behaviours, were
              required to account for stimulus-specificity. Moreover, each
              stimulus evoked more than one behaviour revealing a robust
              one-to-many mapping between sensations and behaviours that could
              not be detected from locomotion data.Our results challenge the
              current view of visually and auditory guided behaviours as purely
              locomotion-based actions (e.g. freeze, escape) and indicate that
              behavioural diversity and sensory specificity unfold in a higher
              dimensional space spanning multiple motor actions.",
  journal  = "bioRxiv",
  pages    = "2020.02.24.961565",
  month    =  mar,
  year     =  2020,
  keywords = "Locomotion",
  language = "en",
  doi      = "10.1101/2020.02.24.961565"
}


@ARTICLE{Cregg2020-ie,
  title    = "Brainstem neurons that command mammalian locomotor asymmetries",
  author   = "Cregg, Jared M and Leiras, Roberto and Montalant, Alexia and
              Wanken, Paulina and Wickersham, Ian R and Kiehn, Ole",
  abstract = "Descending command neurons instruct spinal networks to execute
              basic locomotor functions, such as gait and speed. The command
              functions for gait and speed are symmetric, implying that a
              separate unknown system directs asymmetric movements, including
              the ability to move left or right. In the present study, we
              report that Chx10-lineage reticulospinal neurons act to control
              the direction of locomotor movements in mammals. Chx10 neurons
              exhibit mainly ipsilateral projection, and their selective
              unilateral activation causes ipsilateral turning movements in
              freely moving mice. Unilateral inhibition of Chx10 neurons causes
              contralateral turning movements. Paired left--right motor
              recordings identified distinct mechanisms for directional
              movements mediated via limb and axial spinal circuits. Finally,
              we identify sensorimotor brain regions that project on to Chx10
              reticulospinal neurons, and demonstrate that their unilateral
              activation can impart left--right directional commands. Together
              these data identify the descending motor system that commands
              left--right locomotor asymmetries in mammals.",
  journal  = "Nat. Neurosci.",
  month    =  may,
  year     =  2020,
  issn     = "1097-6256, 1546-1726",
  doi      = "10.1038/s41593-020-0633-7"
}

@UNPUBLISHED{Rayshubskiy2020-ad,
  title    = "Neural control of steering in walking Drosophila",
  author   = "Rayshubskiy, Aleksandr and Holtz, Stephen L and D'Alessandro,
              Isabel and Li, Anna A and Vanderbeck, Quinn X and Haber, Isabel S
              and Gibb, Peter W and Wilson, Rachel I",
  abstract = "During navigation, the brain must continuously integrate external
              guidance cues with internal spatial maps to update steering
              commands. However, it has been difficult to link spatial maps
              with motor control. Here we identify 9descending steering9
              neurons in the Drosophila brain that lie two synapses downstream
              from the brain9s heading direction map in the central complex.
              These steering neurons predict behavioral turns caused by
              microstimulation of the spatial map. Moreover, these neurons
              receive 9direct9 sensory input that bypasses the central complex,
              and they predict steering evoked by multimodal stimuli.
              Unilateral activation of these neurons can promote turning, while
              bilateral silencing interferes with body and leg movements. In
              short, these neurons combine internal maps with external cues to
              predict and influence steering. They represent a key link between
              cognitive maps, which use an abstract coordinate frame, and motor
              commands, which use a body-centric coordinate frame.",
  journal  = "bioRxiv",
  pages    = "2020.04.04.024703",
  month    =  apr,
  year     =  2020,
  language = "en",
  doi      = "10.1101/2020.04.04.024703"
}


@ARTICLE{Remington2018-tc,
  title    = "Flexible Sensorimotor Computations through Rapid Reconfiguration
              of Cortical Dynamics",
  author   = "Remington, Evan D and Narain, Devika and Hosseini, Eghbal A and
              Jazayeri, Mehrdad",
  abstract = "Neural mechanisms that support flexible sensorimotor computations
              are not well understood. In a dynamical system whose state is
              determined by interactions among neurons, computations can be
              rapidly reconfigured by controlling the system's inputs and
              initial conditions. To investigate whether the brain employs such
              control mechanisms, we recorded from the dorsomedial frontal
              cortex of monkeys trained to measure and produce time intervals
              in two sensorimotor contexts. The geometry of neural trajectories
              during the production epoch was consistent with a mechanism
              wherein the measured interval and sensorimotor context exerted
              control over cortical dynamics by adjusting the system's initial
              condition and input, respectively. These adjustments, in turn,
              set the speed at which activity evolved in the production epoch,
              allowing the animal to flexibly produce different time intervals.
              These results provide evidence that the language of dynamical
              systems can be used to parsimoniously link brain activity to
              sensorimotor computations.",
  journal  = "Neuron",
  volume   =  98,
  number   =  5,
  pages    = "1005--1019.e5",
  month    =  jun,
  year     =  2018,
  keywords = "Dynamical Systems; cognitive flexibility; electrophysiology;
              frontal cortex; motor planning; population coding; recurrent
              neural networks; sensorimotor coordination; timing",
  language = "en",
  issn     = "0896-6273, 1097-4199",
  pmid     = "29879384",
  doi      = "10.1016/j.neuron.2018.05.020",
  pmc      = "PMC6009852"
}


@ARTICLE{Grillner2002-si,
  title    = "Cellular bases of a vertebrate locomotor system-steering,
              intersegmental and segmental co-ordination and sensory control",
  author   = "Grillner, Sten and Wall{\'e}n, Peter",
  abstract = "The isolated brainstem-spinal cord of the lamprey is used as an
              experimental model in the analysis of the cellular bases of
              vertebrate locomotor behaviour. In this article we review the
              neural mechanisms involved in the control of steering,
              intersegmental co-ordination, as well as the segmental burst
              generation and the sensory contribution to motor pattern
              generation. Within these four components of the control system
              for locomotion, we now have good knowledge of not only the
              neurones that take part and their synaptic interactions, but also
              the membrane properties of these neurones, including ion channel
              subtypes, and their contribution to motor pattern generation.",
  journal  = "Brain Res. Brain Res. Rev.",
  volume   =  40,
  number   = "1-3",
  pages    = "92--106",
  month    =  oct,
  year     =  2002,
  language = "en",
  pmid     = "12589909",
  doi      = "10.1016/s0165-0173(02)00193-5"
}

@ARTICLE{Saitoh2007-yr,
  title    = "Tectal control of locomotion, steering, and eye movements in
              lamprey",
  author   = "Saitoh, Kazuya and M{\'e}nard, Ariane and Grillner, Sten",
  abstract = "The intrinsic function of the brain stem-spinal cord networks
              eliciting the locomotor synergy is well described in the
              lamprey-a vertebrate model system. This study addresses the role
              of tectum in integrating eye, body orientation, and locomotor
              movements as in steering and goal-directed behavior. Electrical
              stimuli were applied to different areas within the optic tectum
              in head-restrained semi-intact lampreys (n = 40). Motions of the
              eyes and body were recorded simultaneously (videotaped). Brief
              pulse trains (0.5 s) lateral bending movements of the body
              (orientation movements) were added, and with even longer stimuli
              locomotor movements were initiated. Depending on the tectal area
              stimulated, four characteristic response patterns were observed.
              In a lateral area conjugate horizontal eye movements combined
              with lateral bending movements of the body and locomotor
              movements were elicited, depending on stimulus duration. The
              amplitude of the eye movement and bending movements was site
              specific within this region. In a rostromedial area, bilateral
              downward vertical eye movements occurred. In a caudomedial tectal
              area, large-amplitude undulatory body movements akin to
              struggling behavior were elicited, combined with large-amplitude
              eye movements that were antiphasic to the body movements. The
              alternating eye movements were not dependent on vestibuloocular
              reflexes. Finally, in a caudolateral area locomotor movements
              without eye or bending movements could be elicited. These results
              show that tectum can provide integrated motor responses of eye,
              body orientation, and locomotion of the type that would be
              required in goal-directed locomotion.",
  journal  = "J. Neurophysiol.",
  volume   =  97,
  number   =  4,
  pages    = "3093--3108",
  month    =  apr,
  year     =  2007,
  language = "en",
  issn     = "0022-3077",
  pmid     = "17303814",
  doi      = "10.1152/jn.00639.2006"
}

@ARTICLE{Sussillo2013-ey,
  title     = "Opening the black box: low-dimensional dynamics in
               high-dimensional recurrent neural networks",
  author    = "Sussillo, David and Barak, Omri",
  abstract  = "Recurrent neural networks (RNNs) are useful tools for learning
               nonlinear relationships between time-varying inputs and outputs
               with complex temporal dependencies. Recently developed
               algorithms have been successful at training RNNs to perform a
               wide variety of tasks, but the resulting networks have been
               treated as black boxes: their mechanism of operation remains
               unknown. Here we explore the hypothesis that fixed points, both
               stable and unstable, and the linearized dynamics around them,
               can reveal crucial aspects of how RNNs implement their
               computations. Further, we explore the utility of linearization
               in areas of phase space that are not true fixed points but
               merely points of very slow movement. We present a simple
               optimization technique that is applied to trained RNNs to find
               the fixed and slow points of their dynamics. Linearization
               around these slow regions can be used to explore, or
               reverse-engineer, the behavior of the RNN. We describe the
               technique, illustrate it using simple examples, and finally
               showcase it on three high-dimensional RNN examples: a 3-bit
               flip-flop device, an input-dependent sine wave generator, and a
               two-point moving average. In all cases, the mechanisms of
               trained networks could be inferred from the sets of fixed and
               slow points and the linearized dynamics around them.",
  journal   = "Neural Comput.",
  publisher = "MIT Press",
  volume    =  25,
  number    =  3,
  pages     = "626--649",
  month     =  mar,
  year      =  2013,
  keywords  = "RNN",
  language  = "en",
  issn      = "0899-7667, 1530-888X",
  pmid      = "23272922",
  doi       = "10.1162/NECO\_a\_00409"
}


@ARTICLE{Sussillo2014-mo,
  title    = "Neural circuits as computational dynamical systems",
  author   = "Sussillo, David",
  abstract = "Many recent studies of neurons recorded from cortex reveal
              complex temporal dynamics. How such dynamics embody the
              computations that ultimately lead to behavior remains a mystery.
              Approaching this issue requires developing plausible hypotheses
              couched in terms of neural dynamics. A tool ideally suited to aid
              in this question is the recurrent neural network (RNN). RNNs
              straddle the fields of nonlinear dynamical systems and machine
              learning and have recently seen great advances in both theory and
              application. I summarize recent theoretical and technological
              advances and highlight an example of how RNNs helped to explain
              perplexing high-dimensional neurophysiological data in the
              prefrontal cortex.",
  journal  = "Curr. Opin. Neurobiol.",
  volume   =  25,
  pages    = "156--163",
  month    =  apr,
  year     =  2014,
  keywords = "RNN To read;RNN",
  language = "en",
  issn     = "0959-4388, 1873-6882",
  pmid     = "24509098",
  doi      = "10.1016/j.conb.2014.01.008"
}

@ARTICLE{Grillner2020-uq,
  title     = "Current Principles of Motor Control, with Special Reference to
               Vertebrate Locomotion",
  author    = "Grillner, Sten and El Manira, Abdeljabbar",
  abstract  = "The vertebrate control of locomotion involves all levels of the
               nervous system from cortex to the spinal cord. Here, we aim to
               cover all main aspects of this complex behavior, from the
               operation of the microcircuits in the spinal cord to the systems
               and behavioral levels and extend from mammalian locomotion to
               the basic undulatory movements of lamprey and fish. The cellular
               basis of propulsion represents the core of the control system,
               and it involves the spinal central pattern generator networks
               (CPGs) controlling the timing of different muscles, the sensory
               compensation for perturbations, and the brain stem command
               systems controlling the level of activity of the CPGs and the
               speed of locomotion. The forebrain and in particular the basal
               ganglia are involved in determining which motor programs should
               be recruited at a given point of time and can both initiate and
               stop locomotor activity. The propulsive control system needs to
               be integrated with the postural control system to maintain body
               orientation. Moreover, the locomotor movements need to be
               steered so that the subject approaches the goal of the locomotor
               episode, or avoids colliding with elements in the environment or
               simply escapes at high speed. These different aspects will all
               be covered in the review.",
  journal   = "Physiol. Rev.",
  publisher = "physiology.org",
  volume    =  100,
  number    =  1,
  pages     = "271--320",
  month     =  jan,
  year      =  2020,
  keywords  = "basal ganglia; central pattern generators; cerebellum; spinal
               cord; vestibular; visuomotor",
  language  = "en",
  issn      = "0031-9333, 1522-1210",
  pmid      = "31512990",
  doi       = "10.1152/physrev.00015.2019"
}

@ARTICLE{Woon2019-lj,
  title    = "Involvement of the rodent prelimbic and medial orbitofrontal
              cortices in goal-directed action: A brief review",
  author   = "Woon, Ellen P and Sequeira, Michelle K and Barbee, Britton R and
              Gourley, Shannon L",
  abstract = "Goal-directed action refers to selecting behaviors based on the
              expectation that they will be reinforced with desirable outcomes.
              It is typically conceptualized as opposing habit-based behaviors,
              which are instead supported by stimulus-response associations and
              insensitive to consequences. The prelimbic prefrontal cortex (PL)
              is positioned along the medial wall of the rodent prefrontal
              cortex. It is indispensable for action-outcome-driven
              (goal-directed) behavior, consolidating action-outcome
              relationships and linking contextual information with
              instrumental behavior. In this brief review, we will discuss the
              growing list of molecular factors involved in PL function.
              Ventral to the PL is the medial orbitofrontal cortex (mOFC). We
              will also summarize emerging evidence from rodents (complementing
              existing literature describing humans) that it too is involved in
              action-outcome conditioning. We describe experiments using
              procedures that quantify responding based on reward value, the
              likelihood of reinforcement, or effort requirements, touching
              also on experiments assessing food consumption more generally. We
              synthesize these findings with the argument that the mOFC is
              essential to goal-directed action when outcome value information
              is not immediately observable and must be recalled and inferred.",
  journal  = "J. Neurosci. Res.",
  month    =  dec,
  year     =  2019,
  keywords = "action-outcome; contingency degradation; devaluation; habit;
              mouse; rat; response-outcome; review; reward",
  language = "en",
  issn     = "0360-4012, 1097-4547",
  pmid     = "31820488",
  doi      = "10.1002/jnr.24567"
}

@ARTICLE{Kao2019-hv,
  title    = "Considerations in using recurrent neural networks to probe neural
              dynamics",
  author   = "Kao, Jonathan C",
  abstract = "Recurrent neural networks (RNNs) are increasingly being used to
              model complex cognitive and motor tasks performed by behaving
              animals. RNNs are trained to reproduce animal behavior while also
              capturing key statistics of empirically recorded neural activity.
              In this manner, the RNN can be viewed as an in silico circuit
              whose computational elements share similar motifs with the
              cortical area it is modeling. Furthermore, because the RNN's
              governing equations and parameters are fully known, they can be
              analyzed to propose hypotheses for how neural populations
              compute. In this context, we present important considerations
              when using RNNs to model motor behavior in a delayed reach task.
              First, by varying the network's nonlinear activation and rate
              regularization, we show that RNNs reproducing single-neuron
              firing rate motifs may not adequately capture important
              population motifs. Second, we find that even when RNNs reproduce
              key neurophysiological features on both the single neuron and
              population levels, they can do so through distinctly different
              dynamical mechanisms. To distinguish between these mechanisms, we
              show that an RNN consistent with a previously proposed dynamical
              mechanism is more robust to input noise. Finally, we show that
              these dynamics are sufficient for the RNN to generalize to tasks
              it was not trained on. Together, these results emphasize
              important considerations when using RNN models to probe neural
              dynamics.NEW \& NOTEWORTHY Artificial neurons in a recurrent
              neural network (RNN) may resemble empirical single-unit activity
              but not adequately capture important features on the neural
              population level. Dynamics of RNNs can be visualized in
              low-dimensional projections to provide insight into the RNN's
              dynamical mechanism. RNNs trained in different ways may reproduce
              neurophysiological motifs but do so with distinctly different
              mechanisms. RNNs trained to only perform a delayed reach task can
              generalize to perform tasks where the target is switched or the
              target location is changed.",
  journal  = "J. Neurophysiol.",
  volume   =  122,
  number   =  6,
  pages    = "2504--2521",
  month    =  dec,
  year     =  2019,
  keywords = "artificial neural network; motor cortex; neural computation;
              neural dynamics; recurrent neural network;RNN To read;RNN",
  language = "en",
  issn     = "0022-3077, 1522-1598",
  pmid     = "31619125",
  doi      = "10.1152/jn.00467.2018"
}


@ARTICLE{Kao2019-wk,
  title    = "Neuroscience out of control: control-theoretic perspectives on
              neural circuit dynamics",
  author   = "Kao, Ta-Chu and Hennequin, Guillaume",
  abstract = "A major challenge in systems neuroscience is to understand how
              the dynamics of neural circuits give rise to behaviour. Analysis
              of complex dynamical systems is also at the heart of control
              engineering, where it is central to the design of robust control
              strategies. Although a rich engineering literature has grown over
              decades to facilitate the analysis of such systems, little of it
              has percolated into neuroscience so far. Here, we give a brief
              introduction to a number of core control-theoretic concepts that
              provide useful perspectives on neural circuit dynamics. We
              introduce important mathematical tools related to these concepts,
              and establish connections to neural circuit analysis, focusing on
              a number of themes that have arisen from the modern 'state-space'
              view on neural population dynamics.",
  journal  = "Curr. Opin. Neurobiol.",
  volume   =  58,
  pages    = "122--129",
  month    =  oct,
  year     =  2019,
  language = "en",
  issn     = "0959-4388, 1873-6882",
  pmid     = "31563084",
  doi      = "10.1016/j.conb.2019.09.001"
}


@INCOLLECTION{Nitz2014-ca,
  title     = "The Posterior Parietal Cortex: Interface Between Maps of
               External Spaces and the Generation of Action Sequences",
  booktitle = "{Space,Time} and Memory in the Hippocampal Formation",
  author    = "Nitz, Douglas A",
  editor    = "Derdikman, Dori and Knierim, James J",
  abstract  = "In primates as well as rodents, the posterior parietal cortex
               maps spatial relationships having both egocentric and external
               frames of reference. In this chapter, the form in which rat
               posterior parietal cortex neuronal activity maps position within
               trajectories through the environment is considered in detail and
               compared to the forms of spatial mapping observed for neurons of
               the hippocampus and entorhinal cortex. Evidence is presented to
               indicate that posterior parietal neurons simultaneously map
               positions both within and across segments of paths through an
               environment. It is suggested that the specific nature of
               posterior parietal cortex mapping of space serves, in part, to
               transition knowledge of position in the environment, given by
               hippocampus and entorhinal cortex, into efficient path-running
               behavior via projections to primary and secondary sensory and
               motor cortices. Posterior parietal cortex activity is also
               hypothesized to play a role both in driving trajectory
               dependence of hippocampal place cells and in anchoring spatially
               specific hippocampal and entorhinal cortical activity to the
               boundaries of the observable environment.",
  publisher = "Springer Vienna",
  pages     = "27--54",
  year      =  2014,
  address   = "Vienna",
  keywords  = "Spatial Navigation;Authors/Nitz",
  isbn      = "9783709112922",
  doi       = "10.1007/978-3-7091-1292-2\_2"
}

@ARTICLE{Nitz2009-vz,
  title    = "Parietal cortex, navigation, and the construction of arbitrary
              reference frames for spatial information",
  author   = "Nitz, Douglas",
  abstract = "The registration of spatial information by neurons of the
              parietal cortex takes on many forms. In most experiments,
              spatially modulated parietal activity patterns are found to take
              as their frame of reference some part of the body such as the
              retina. However, recent findings obtained in single neuron
              recordings from both rat and monkey parietal cortex suggest that
              the frame of reference utilized by parietal cortex may also be
              abstract or arbitrary in nature. Evidence in rats comes from work
              indicating that parietal activity in freely behaving rodents is
              organized according to the space defined by routes taken through
              an environment. In monkeys, evidence for an object-centered frame
              of reference has recently been presented. The present work
              reviews single neuron recording experiments in parietal cortex of
              freely behaving rats and considers the potential contribution of
              parietal cortex in solving navigational tasks. It is proposed
              that parietal cortex, in interaction with the hippocampus, plays
              a critical role in the selection of the most appropriate route
              between two points and, in addition, produces a route-based
              positional signal capable of guiding sensorimotor transitions.",
  journal  = "Neurobiol. Learn. Mem.",
  volume   =  91,
  number   =  2,
  pages    = "179--185",
  month    =  feb,
  year     =  2009,
  keywords = "navigation;Spatial Navigation;Authors/Nitz",
  language = "en",
  issn     = "1074-7427, 1095-9564",
  pmid     = "18804545",
  doi      = "10.1016/j.nlm.2008.08.007"
}

@ARTICLE{Nitz2006-mn,
  title    = "Tracking route progression in the posterior parietal cortex",
  author   = "Nitz, Douglas A",
  abstract = "Quick and efficient traversal of learned routes is critical to
              the survival of many animals. Routes can be defined by both the
              ordering of navigational epochs, such as continued forward motion
              or execution of a turn, and the distances separating them. The
              neural substrates conferring the ability to fluidly traverse
              complex routes are not well understood, but likely entail
              interactions between frontal, parietal, and rhinal cortices and
              the hippocampus. This paper demonstrates that posterior parietal
              cortical neurons map both individual and multiple navigational
              epochs with respect to their order in a route. In direct contrast
              to spatial firing patterns of hippocampal neurons, parietal
              neurons discharged in a place- and direction-independent fashion.
              Parietal route maps were scalable and versatile in that they were
              independent of the size and spatial configuration of navigational
              epochs. The results provide a framework in which to consider
              parietal function in spatial cognition.",
  journal  = "Neuron",
  volume   =  49,
  number   =  5,
  pages    = "747--756",
  month    =  mar,
  year     =  2006,
  keywords = "navigation;Spatial Navigation;Authors/Nitz",
  language = "en",
  issn     = "0896-6273",
  pmid     = "16504949",
  doi      = "10.1016/j.neuron.2006.01.037"
}