From 9d857211dd3b088415dc878397200cca5f3b8435 Mon Sep 17 00:00:00 2001 From: ackman678 Date: Mon, 29 Mar 2021 11:31:20 -0700 Subject: [PATCH] sbib and csl --- OMEGA.bib | 1166 ++++++++++++++++++++++++++++++++++++++++++++++-- README.md | 6 +- bibd-md.csl | 335 ++++++++++++++ bibd-plain.csl | 333 ++++++++++++++ bibd.csl | 335 ++++++++++++++ 5 files changed, 2138 insertions(+), 37 deletions(-) create mode 100644 bibd-md.csl create mode 100644 bibd-plain.csl create mode 100644 bibd.csl diff --git a/OMEGA.bib b/OMEGA.bib index 72cb2b4..dc06958 100644 --- a/OMEGA.bib +++ b/OMEGA.bib @@ -170,7 +170,7 @@ Year = {2015}, File = {papers/Shadrin_SciRep2015.pdf}} -@article{10.7554/eLife.28158, +@article{Cong2017, Abstract = {The internal brain dynamics that link sensation and action are arguably better studied during natural animal behaviors. Here, we report on a novel volume imaging and 3D tracking technique that monitors whole brain neural activity in freely swimming larval zebrafish (\textit{Danio rerio}). We demonstrated the capability of our system through functional imaging of neural activity during visually evoked and prey capture behaviors in larval zebrafish.}, Article_Type = {journal}, Author = {Cong, Lin and Wang, Zeguan and Chai, Yuming and Hang, Wei and Shang, Chunfeng and Yang, Wenbin and Bai, Lu and Du, Jiulin and Wang, Kai and Wen, Quan}, @@ -212,7 +212,7 @@ Year = {2016}, File = {papers/Itzhaki_JAlzheimersDis2016.pdf}} -@article{10.7554/eLife.35261, +@article{Barchini2018, Abstract = {Detection of salient objects in the visual scene is a vital aspect of an animal's interactions with its environment. Here, we show that neurons in the mouse superior colliculus (SC) encode visual saliency by detecting motion contrast between stimulus center and surround. Excitatory neurons in the most superficial lamina of the SC are contextually modulated, monotonically increasing their response from suppression by the same-direction surround to maximal potentiation by an oppositely-moving surround. The degree of this potentiation declines with depth in the SC. Inhibitory neurons are suppressed by any surround at all depths. These response modulations in both neuronal populations are much more prominent to direction contrast than to phase, temporal frequency, or static orientation contrast, suggesting feature-specific saliency encoding in the mouse SC. Together, our findings provide evidence supporting locally generated feature representations in the SC, and lay the foundations towards a mechanistic and evolutionary understanding of their emergence.}, Article_Type = {journal}, Author = {Barchini, Jad and Shi, Xuefeng and Chen, Hui and Cang, Jianhua}, @@ -523,24 +523,6 @@ Year = {2010}, File = {papers/DeBiase_JNeurosci2010.pdf}} -@article{Brown:2001a, - Abstract = {'Independent component analysis' is a technique of data transformation that finds independent sources of activity in recorded mixtures of sources. It can be used to recover fluctuations of membrane potential from individual neurons in multiple-detector optical recordings. There are some examples in which more than 100 neurons can be separated simultaneously. Independent component analysis automatically separates overlapping action potentials, recovers action potentials of different sizes from the same neuron, removes artifacts and finds the position of each neuron on the detector array. One limitation is that the number of sources--neurons and artifacts--must be equal to or less than the number of simultaneous recordings. Independent component analysis also has many other applications in neuroscience including, removal of artifacts from EEG data, identification of spatially independent brain regions in fMRI recordings and determination of population codes in multi-unit recordings.}, - Author = {Brown, G D and Yamada, S and Sejnowski, T J}, - Date-Added = {2018-02-28 22:03:12 +0000}, - Date-Modified = {2018-02-28 22:03:12 +0000}, - Journal = {Trends Neurosci}, - Journal-Full = {Trends in neurosciences}, - Mesh = {Action Potentials; Algorithms; Animals; Brain; Electroencephalography; Humans; Linear Models; Membrane Potentials; Models, Neurological; Neurons}, - Month = {Jan}, - Number = {1}, - Pages = {54-63}, - Pmid = {11163888}, - Pst = {ppublish}, - Title = {Independent component analysis at the neural cocktail party}, - Volume = {24}, - Year = {2001}, - File = {papers/Brown_TrendsNeurosci2001a.pdf}} - @article{Beier:2013, Abstract = {The use of neurotropic viruses as transsynaptic tracers was first described in the 1960s, but only recently have such viruses gained popularity as a method for labeling neural circuits. The development of retrograde monosynaptic tracing vectors has enabled visualization of the presynaptic sources onto defined sets of postsynaptic neurons. Here, we describe the first application of a novel viral tracer, based on vesicular stomatitis virus (VSV), which directs retrograde transsynaptic viral spread between defined cell types. We use this virus in the mouse retina to show connectivity between starburst amacrine cells (SACs) and their known synaptic partners, direction-selective retinal ganglion cells, as well as to discover previously unknown connectivity between SACs and other retinal ganglion cell types. These novel connections were confirmed using physiological recordings. VSV transsynaptic tracing enables cell type-specific dissection of neural circuitry and can reveal synaptic relationships among neurons that are otherwise obscured due to the complexity and density of neuropil.}, Author = {Beier, Kevin T and Borghuis, Bart G and El-Danaf, Rana N and Huberman, Andrew D and Demb, Jonathan B and Cepko, Constance L}, @@ -6095,7 +6077,7 @@ CONCLUSIONS: We suggest that AEDs that increase the extracellular concentration Year = {2012}, File = {papers/Ichinohe_FrontNeuroanat2012.pdf}} -@article{Murakami:2015, +@article{Murakami2015, Abstract = {Due to recent advances of genetic manipulation, mouse brain has become a useful model for studying brain function, which demands whole brain functional mapping techniques in the mouse brain. In the present study, to finely map visual responsive areas in the mouse brain, we combined high-resolution wide-field optical imaging with transgenic mice containing the genetically encoded Ca(2+) indicator, GCaMP3. With the high signal amplitude of GCaMP3 expressing in excitatory neurons, this system allowed neural activity to be observed with relatively fine spatial resolution and cell-type specificity. To evaluate this system, we examined whether non-visual areas exhibited a visual response over the entire surface of the mouse hemisphere. We found that two association areas, the retrosplenial area (RS) and secondary motor/anterior cingulate area (M2/AC), were significantly responsive to drifting gratings. Examination using gratings with distinct spatiotemporal frequency parameters revealed that the RS strongly responded to high-spatial and low-temporal frequency gratings. The M2/AC exhibited a response property similar to that of the RS, though it was not statistically significant. Finally, we performed cellular imaging using two-photon microscopy to examine orientation and direction selectivity of individual neurons, and found that a minority of neurons in the RS clearly showed visual responses sharply selective for orientation and direction. These results suggest that neurons in RS encode visual information of fine spatial details in images. Thus, the present study shows the usefulness of the functional mapping method using a combination of wide-field and two-photon Ca(2+) imaging, which allows for whole brain mapping with high spatiotemporal resolution and cell-type specificity.}, Author = {Murakami, Tomonari and Yoshida, Takashi and Matsui, Teppei and Ohki, Kenichi}, Date-Added = {2017-04-18 20:16:45 +0000}, @@ -9924,18 +9906,45 @@ VIDEO ABSTRACT: }, Year = {1962}, File = {papers/BASSER_Brain1962.pdf}} -@article{Ackman:2014c, +@article{Ackman2014c, Abstract = {The cerebral cortex exhibits spontaneous and sensory evoked patterns of activity during early development that is vital for the formation and refinement of neural circuits. Identifying the source and flow of this activity locally and globally is critical for understanding principles guiding self-organization in the developing brain. Here we use whole brain transcranial optical imaging at high spatial and temporal resolution to demonstrate that dynamical patterns of neuronal activity in developing mouse neocortex consist of spatially discrete domains that are coordinated in an age, areal, and behavior- dependent fashion. Ongoing cortical activity displays mirror-symmetric activation patterns across the cerebral hemispheres and stereotyped network architectures that are shaped during development, with parietal-sensorimotor subnetworks functionally connected to occipital regions through frontal-medial cortical areas. This study provides the first broad description of population activity in the developing neocortex at a scope and scale that bridges the microscopic and macroscopic spatiotemporal resolutions provided by traditional neurophysiological and functional neuroimaging techniques. Mesoscale maps of cortical population dynamics within animal models will be crucial for future efforts to understand and treat neurodevelopmental disorders.}, Author = {Ackman, James B and Zeng, Hongkui and Crair, Michael C}, Date-Added = {2014-12-10 16:14:44 +0000}, Date-Modified = {2017-12-01 02:11:23 +0000}, Doi = {10.1101/012237}, Journal = {bioRxiv}, + publisher = {Cold Spring Harbor Laboratory}, Month = {Dec}, Title = {Structured dynamics of neural activity across developing neocortex}, Year = {2014}, File = {papers/Ackman_bioRxiv2014.pdf}, - Bdsk-Url-1 = {http://dx.doi.org/10.1101/012237}} + url = {http://dx.doi.org/10.1101/012237}, + eprint = {https://www.biorxiv.org/content/early/2014/12/05/012237.full.pdf}} + +@article{Mullen2021, + author = {Mullen, Brian R. and Weiser, Sydney C. and Ascencio, Desiderio and Ackman, James B.}, + title = {Automated classification of signal sources in mesoscale calcium imaging}, + elocation-id = {2021.02.23.432573}, + year = {2021}, + doi = {10.1101/2021.02.23.432573}, + publisher = {Cold Spring Harbor Laboratory}, + abstract = {Functional imaging of neural cell populations is critical for mapping intra- and inter-regional network dynamics across the neocortex. Recently we showed that an unsupervised machine learning decomposition of densely sampled recordings of cortical calcium dynamics results in a collection of components comprised of neuronal signal sources distinct from optical, movement, and vascular artifacts. Here we build a supervised learning classifier that automatically separates neural activity and artifact components, using a set of extracted spatial and temporal metrics that characterize the respective components. We demonstrate that the performance of the machine classifier matches human identification of signal components in novel data sets. Further, we analyze control data recorded in glial cell reporter and non-fluorescent mouse lines that validates human and machine identification of functional component class. This combined workflow of data-driven video decomposition and machine classification of signal sources will aid robust and scalable mapping of complex cerebral dynamics.Competing Interest StatementThe authors have declared no competing interest.}, + URL = {https://www.biorxiv.org/content/10.1101/2021.02.23.432573v1}, + eprint = {https://www.biorxiv.org/content/10.1101/2021.02.23.432573v1.full.pdf}, + journal = {bioRxiv} +} + +@article{Weiser2020, + author = {Weiser, Sydney C. and Mullen, Brian R. and Ascencio, Desiderio and Ackman, James B.}, + title = {Data-driven filtration and segmentation of mesoscale neural dynamics}, + elocation-id = {2020.12.30.424865}, + year = {2021}, + doi = {10.1101/2020.12.30.424865}, + publisher = {Cold Spring Harbor Laboratory}, + abstract = {Recording neuronal group activity across the cortical hemispheres from awake, behaving mice is essential for understanding information flow across cerebral networks. Video recordings of cerebral function comes with challenges, including optical and movement-associated vessel artifacts, and limited references for time series extraction. Here we present a data-driven workflow that isolates artifacts from calcium activity patterns, and segments independent functional units across the cortical surface. Independent Component Analysis utilizes the statistical interdependence of pixel activation to completely unmix signals from background noise, given sufficient spatial and temporal samples. We also utilize isolated signal components to produce segmentations of the cortical surface, unique to each individual{\textquoteright}s functional patterning. Time series extraction from these maps maximally represent the underlying signal in a highly compressed format. These improved techniques for data pre-processing, spatial segmentation, and time series extraction result in optimal signals for further analysis.}, + url = {https://www.biorxiv.org/content/10.1101/2020.12.30.424865v2}, + eprint = {https://www.biorxiv.org/content/10.1101/2020.12.30.424865v2.full.pdf}, + journal = {bioRxiv}} @article{Sakaki:1997, Abstract = {Depletion of intracellular Ca2+ stores induces a capacitative Ca2+ influx in non-neural cells. It has been unknown whether the capacitative Ca2+ influx occurs in the cells of nervous systems. We found the capacitative Ca2+ influx in the neural retina of early embryonic chick with Fura-2 fluorescence measurements. A Ca(2+)-free medium containing thapsigargin (500 nM), an inhibitor of Ca(2+)-ATPase of intracellular Ca2+ stores, was applied to the neural retina of embryonic day 3 (E3) chick. A rise in intracellular Ca2+ concentration was evoked after the reintroduction of extracellular Ca2+, and this Ca2+ rise was suppressed by Zn2+ (1 mM) and Ni2+ (5 mM). The developmental changes in the Ca2+ rise induced by thapsigargin (250 nM) were studied from E3 to E13. The thapsigargin-induced Ca2+ rise was largest at E3, declined rapidly toward E6, and then decreased gradually until E13, when the Ca2+ rise almost disappeared. This developmental profile correlated with the decline in the mitotic activities of the retinal cells studied by Prada et al. The fluorescence imaging with the vertical slice of the E9 retina showed that the site at which the thapsigargin-induced Ca2+ rise was largest was the most outer layer of the retina, where proliferating cells are located. This spatial distribution and the above developmental profile may suggest that the capacitative Ca2+ influx occurs at the early period of neurogenesis when the cells have mitotic activities.}, @@ -24727,7 +24736,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a Volume = {12}, Year = {1989}, File = {papers/Tsien_AnnuRevNeurosci1989.pdf}, - Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.ne.12.030189.001303}} + Url = {http://dx.doi.org/10.1146/annurev.ne.12.030189.001303}} @article{Tsien:1990, Author = {Tsien, R W and Tsien, R Y}, @@ -24744,7 +24753,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a Volume = {6}, Year = {1990}, File = {papers/Tsien_AnnuRevCellBiol1990.pdf}, - Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.cb.06.110190.003435}} + Url = {http://dx.doi.org/10.1146/annurev.cb.06.110190.003435}} @article{Miyawaki:1997, Abstract = {Important Ca2+ signals in the cytosol and organelles are often extremely localized and hard to measure. To overcome this problem we have constructed new fluorescent indicators for Ca2+ that are genetically encoded without cofactors and are targetable to specific intracellular locations. We have dubbed these fluorescent indicators 'cameleons'. They consist of tandem fusions of a blue- or cyan-emitting mutant of the green fluorescent protein (GFP), calmodulin, the calmodulin-binding peptide M13, and an enhanced green- or yellow-emitting GFP. Binding of Ca2+ makes calmodulin wrap around the M13 domain, increasing the fluorescence resonance energy transfer (FRET) between the flanking GFPs. Calmodulin mutations can tune the Ca2+ affinities to measure free Ca2+ concentrations in the range 10(-8) to 10(-2) M. We have visualized free Ca2+ dynamics in the cytosol, nucleus and endoplasmic reticulum of single HeLa cells transfected with complementary DNAs encoding chimaeras bearing appropriate localization signals. Ca2+ concentration in the endoplasmic reticulum of individual cells ranged from 60 to 400 microM at rest, and 1 to 50 microM after Ca2+ mobilization. FRET is also an indicator of the reversible intermolecular association of cyan-GFP-labelled calmodulin with yellow-GFP-labelled M13. Thus FRET between GFP mutants can monitor localized Ca2+ signals and protein heterodimerization in individual live cells.}, @@ -24860,7 +24869,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a Volume = {324}, Year = {1986}, File = {papers/Grinvald_Nature1986.pdf}, - Bdsk-Url-1 = {http://dx.doi.org/10.1038/324361a0}} + Url = {http://dx.doi.org/10.1038/324361a0}} @article{Xu:2007a, Abstract = {Neuronal interactions between primary and secondary visual cortical areas are important for visual processing, but the spatiotemporal patterns of the interaction are not well understood. We used voltage-sensitive dye imaging to visualize neuronal activity in rat visual cortex and found visually evoked waves propagating from V1 to other visual areas. A primary wave originated in the monocular area of V1 and was "compressed" when propagating to V2. A reflected wave initiated after compression and propagated backward into V1. The compression occurred at the V1/V2 border, and local GABAA inhibition is important for the compression. The compression/reflection pattern provides a two-phase modulation: V1 is first depolarized by the primary wave, and then V1 and V2 are simultaneously depolarized by the reflected and primary waves, respectively. The compression/reflection pattern only occurred for evoked waves and not for spontaneous waves, suggesting that it is organized by an internal mechanism associated with visual processing.}, @@ -26894,7 +26903,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a Volume = {5}, Year = {2004}, File = {papers/Grinvald_NatRevNeurosci2004.pdf}, - Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn1536}} + Url = {http://dx.doi.org/10.1038/nrn1536}} @article{Homma:2009, Abstract = {This chapter presents three examples of imaging brain activity with voltage- or calcium-sensitive dyes. Because experimental measurements are limited by low sensitivity, the chapter then discusses the methodological aspects that are critical for optimal signal-to-noise ratio. Two of the examples use wide-field (1-photon) imaging and the third uses two-photon scanning microscopy. These methods have relatively high temporal resolution ranging from 10 to 10,000 Hz. The three examples are the following: (1) Internally injected voltage-sensitive dye can be used to monitor membrane potential in the dendrites of invertebrate and vertebrate neurons in in vitro preparations. These experiments are directed at understanding how individual neurons convert the complex input synaptic activity into the output spike train. (2) Recently developed methods for staining many individual cells in the mammalian brain with calcium-sensitive dyes together with two-photon microscopy made it possible to follow the spike activity of many neurons simultaneously while in vivo preparations are responding to stimulation. (3) Calcium-sensitive dyes that are internalized into olfactory receptor neurons in the nose will, after several days, be transported to the nerve terminals of these cells in the olfactory bulb glomeruli. There, the population signals can be used as a measure of the input from the nose to the bulb. Three kinds of noise in measuring light intensity are discussed: (1) Shot noise from the random emission of photons from the preparation. (2) Extraneous (technical) noise from external sources. (3) Noise that occurs in the absence of light, the dark noise. In addition, we briefly discuss the light sources, the optics, and the detectors and cameras. The commonly used organic voltage and ion sensitive dyes stain all of the cell types in the preparation indiscriminately. A major effort is underway to find methods for staining individual cell types in the brain selectively. Most of these efforts center around fluorescent protein activity sensors because transgenic methods can be used to express them in individual cell types.}, @@ -28410,7 +28419,6 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a Abstract = {Spatial navigation is often used as a behavioral task in studies of the neuronal circuits that underlie cognition, learning and memory in rodents. The combination of in vivo microscopy with genetically encoded indicators has provided an important new tool for studying neuronal circuits, but has been technically difficult to apply during navigation. Here we describe methods for imaging the activity of neurons in the CA1 region of the hippocampus with subcellular resolution in behaving mice. Neurons that expressed the genetically encoded calcium indicator GCaMP3 were imaged through a chronic hippocampal window. Head-restrained mice performed spatial behaviors in a setup combining a virtual reality system and a custom-built two-photon microscope. We optically identified populations of place cells and determined the correlation between the location of their place fields in the virtual environment and their anatomical location in the local circuit. The combination of virtual reality and high-resolution functional imaging should allow a new generation of studies to investigate neuronal circuit dynamics during behavior.}, Author = {Dombeck, Daniel A and Harvey, Christopher D and Tian, Lin and Looger, Loren L and Tank, David W}, Date-Added = {2011-03-07 16:22:58 -0500}, - Date-Modified = {2011-09-12 11:19:13 -0400}, Journal = {Nat Neurosci}, Journal-Full = {Nature neuroscience}, Keywords = {optical physiology;calcium imaging; Technique;imaging;in vivo;Optics;microscopy;Multiphoton}, @@ -28424,14 +28432,13 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a Title = {Functional imaging of hippocampal place cells at cellular resolution during virtual navigation}, Volume = {13}, Year = {2010}, - File = {papers/Dombeck_NatNeurosci2010.pdf}, - Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.2648}} + doi = {10.1038/nn.2648}, + File = {papers/Dombeck_NatNeurosci2010.pdf}} @article{Mukamel:2009, Abstract = {Recent advances in fluorescence imaging permit studies of Ca(2+) dynamics in large numbers of cells, in anesthetized and awake behaving animals. However, unlike for electrophysiological signals, standardized algorithms for assigning optically recorded signals to individual cells have not yet emerged. Here, we describe an automated sorting procedure that combines independent component analysis and image segmentation for extracting cells' locations and their dynamics with minimal human supervision. In validation studies using simulated data, automated sorting significantly improved estimation of cellular signals compared to conventional analysis based on image regions of interest. We used automated procedures to analyze data recorded by two-photon Ca(2+) imaging in the cerebellar vermis of awake behaving mice. Our analysis yielded simultaneous Ca(2+) activity traces for up to >100 Purkinje cells and Bergmann glia from single recordings. Using this approach, we found microzones of Purkinje cells that were stable across behavioral states and in which synchronous Ca(2+) spiking rose significantly during locomotion.}, Author = {Mukamel, Eran A and Nimmerjahn, Axel and Schnitzer, Mark J}, Date-Added = {2011-03-07 16:21:59 -0500}, - Date-Modified = {2011-09-12 11:19:13 -0400}, Journal = {Neuron}, Journal-Full = {Neuron}, Keywords = {optical physiology; calcium imaging; Technique;Software;Computational Biology}, @@ -28445,8 +28452,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a Volume = {63}, Year = {2009}, File = {papers/Mukamel_Neuron2009.pdf}, - Bdsk-File-2 = {papers/Mukamel_Neuron2009a.pdf}, - Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2009.08.009}} + doi = {10.1016/j.neuron.2009.08.009}} @article{Coombs:2007, Abstract = {Quantitative methods were used to assess dendritic stratification and other structural features of developing mouse retinal ganglion cells from birth to after eye opening. Cells were labeled by transgenic expression of yellow fluorescent protein, DiOlistics or diffusion of DiI, and subsequently imaged in three dimensions on a confocal microscope followed by morphometric analysis of 13 different structural properties. At postnatal day 1 (P1), the dendrites of all cells ramified across the vertical extent of the inner plexiform layer (IPL). By P3/4, dendrites were largely confined to different strata of the IPL. The stratification of dendrites initially reflected a retraction of widely ramifying dendritic processes, but for the most part this was due to the subsequent vertical expansion of the IPL. By P8, distinct cell classes could be recognized, although these had not yet attained adult-like properties. The structural features differentiating cell classes were found to follow three different developmental trends. The mean values of one set of morphological parameters were essentially unchanged throughout postnatal development; another set of measures showed a rapid rise with age to adult values; and a third set of measures first increased with age and later decreased, with the regressive events initiated around the time of eye opening. These findings suggest that the morphological development of retinal ganglion cells is regulated by diverse factors operating during different but overlapping time periods. Our results also suggest that dendritic stratification may be more highly specified in the developing mammalian retina than has been previously realized.}, @@ -105335,7 +105341,7 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a Uuid = {7DDDA35F-289A-4EC1-8D87-95DDEC11F019}, Volume = {32}, Year = {2001}, - Bdsk-Url-1 = {http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&dopt=r&uid=11719211}} + Url = {http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&dopt=r&uid=11719211}} @article{Waclaw:2006, Abstract = {The molecular mechanisms that regulate the production and diversity of olfactory bulb interneurons remain poorly understood. With the exception of the GABAergic/dopaminergic subtype in the glomerular layer, no information exists concerning the generation of the other subtypes. Here we show that the recently identified zinc finger transcription factor Sp8 is expressed in neurogenic regions, which give rise to olfactory bulb interneurons at embryonic and postnatal time points and remains expressed in the calretinin-expressing and GABAergic/nondopaminergic interneurons of the glomerular layer. Conditional inactivation of Sp8 in the embryonic ventral telencephalon reveals a requirement for the normal generation of these interneuron subtypes. Sp8 conditional mutants exhibit an increase in cell death within the lateral ganglionic eminence and rostral migratory stream. Moreover, mutant neuroblasts/interneurons are misspecified and display abnormal migration patterns in the olfactory bulb, indicating that Sp8 contributes to olfactory bulb interneuron diversity by regulating the survival, migration, and molecular specification of neuroblasts/interneurons.}, @@ -111679,3 +111685,1095 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a nlmuniqueid = {101282001} } + +@article{Xiao2017, + title = {Mapping cortical mesoscopic networks of single spiking cortical or sub-cortical neurons.}, + author = {Xiao, Dongsheng and Vanni, Matthieu P and Mitelut, Catalin C and Chan, Allen W and LeDue, Jeffrey M and Xie, Yicheng and Chen, Andrew Cn and Swindale, Nicholas V and Murphy, Timothy H}, + journal = {Elife}, + volume = {6}, + year = {2017}, + month = {02}, + pages = {}, + abstract = {Understanding the basis of brain function requires knowledge of cortical operations over wide-spatial scales, but also within the context of single neurons. In vivo, wide-field GCaMP imaging and sub-cortical/cortical cellular electrophysiology were used in mice to investigate relationships between spontaneous single neuron spiking and mesoscopic cortical activity. We make use of a rich set of cortical activity motifs that are present in spontaneous activity in anesthetized and awake animals. A mesoscale spike-triggered averaging procedure allowed the identification of motifs that are preferentially linked to individual spiking neurons by employing genetically targeted indicators of neuronal activity. Thalamic neurons predicted and reported specific cycles of wide-scale cortical inhibition/excitation. In contrast, spike-triggered maps derived from single cortical neurons yielded spatio-temporal maps expected for regional cortical consensus function. This approach can define network relationships between any point source of neuronal spiking and mesoscale cortical maps.}, + keywords = {functional connectivity; mesoscale maps; mouse; neuroscience; spike triggered maps; thalamocortical; Action Potentials; Anesthesia; Animals; Brain Mapping; Calcium; Calcium Signaling; Cerebral Cortex; Electrodes, Implanted; Male; Mice; Mice, Transgenic; Molecular Probes; Nerve Net; Neurons; Optical Imaging; Stereotaxic Techniques; Thalamus; Wakefulness; }, + pubmed = {28160463}, + doi = {10.7554/eLife.19976}, + pmc = {PMC5328594}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/28160463}, + file = {papers/Xiao_Elife2017-28160463.pdf}, + nlmuniqueid = {101579614} +} + +@article {Barson468348, + author = {Barson, D and Hamodi, AS and Shen, X and Lur, G and Constable, RT and Cardin, JA and Crair, MC and Higley, MJ}, + title = {Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits}, + elocation-id = {468348}, + year = {2018}, + doi = {10.1101/468348}, + publisher = {Cold Spring Harbor Laboratory}, + abstract = {Spontaneous and sensory-evoked activity propagates across spatial scales in the mammalian cortex but technical challenges have generally precluded establishing conceptual links between the function of local circuits of neurons and brain-wide network dynamics. To solve this problem, we developed a method for simultaneous cellular-resolution two-photon calcium imaging of a local microcircuit and mesoscopic widefield calcium imaging of the entire cortical mantle in awake, behaving mice. Our method employs an orthogonal axis design whereby the mesoscopic objective is oriented downward directly above the brain and the two-photon objective is oriented horizontally, with imaging performed through a glass right angle microprism implanted in the skull. In support of this method, we introduce a suite of analysis tools for relating the activity of individual cells to distal cortical areas, as well as a viral method for robust and widespread gene delivery in the juvenile mouse brain. We use these methods to characterize the diversity of associations of individual, genetically-defined neurons with cortex-wide network motifs.}, + URL = {https://www.biorxiv.org/content/early/2018/11/11/468348}, + eprint = {https://www.biorxiv.org/content/early/2018/11/11/468348.full.pdf}, + journal = {bioRxiv} +} + +@article{Manita2015, + title = {A Top-Down Cortical Circuit for Accurate Sensory Perception.}, + author = {Manita, Satoshi and Suzuki, Takayuki and Homma, Chihiro and Matsumoto, Takashi and Odagawa, Maya and Yamada, Kazuyuki and Ota, Keisuke and Matsubara, Chie and Inutsuka, Ayumu and Sato, Masaaki and Ohkura, Masamichi and Yamanaka, Akihiro and Yanagawa, Yuchio and Nakai, Junichi and Hayashi, Yasunori and Larkum, Matthew E and Murayama, Masanori}, + journal = {Neuron}, + volume = {86}, + number = {5}, + year = {2015}, + month = {Jun}, + pages = {1304-16}, + abstract = {A fundamental issue in cortical processing of sensory information is whether top-down control circuits from higher brain areas to primary sensory areas not only modulate but actively engage in perception. Here, we report the identification of a neural circuit for top-down control in the mouse somatosensory system. The circuit consisted of a long-range reciprocal projection between M2 secondary motor cortex and S1 primary somatosensory cortex. In vivo physiological recordings revealed that sensory stimulation induced sequential S1 to M2 followed by M2 to S1 neural activity. The top-down projection from M2 to S1 initiated dendritic spikes and persistent firing of S1 layer 5 (L5) neurons. Optogenetic inhibition of M2 input to S1 decreased L5 firing and the accurate perception of tactile surfaces. These findings demonstrate that recurrent input to sensory areas is essential for accurate perception and provide a physiological model for one type of top-down control circuit. }, + pubmed = {26004915}, + pii = {S0896-6273(15)00413-4}, + doi = {10.1016/j.neuron.2015.05.006}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/26004915}, + file = {papers/Manita_Neuron2015-26004915.pdf}, + nlmuniqueid = {8809320} +} + +@article{Heiligenberg1991, + title = {The neural basis of behavior: a neuroethological view.}, + author = {Heiligenberg, W}, + journal = {Annu Rev Neurosci}, + volume = {14}, + year = {1991}, + pages = {247-67}, + pubmed = {2031571}, + doi = {10.1146/annurev.ne.14.030191.001335}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/2031571}, + file = {papers/Heiligenberg_AnnuRevNeurosci1991-2031571.pdf}, + nlmuniqueid = {7804039} +} + +@article{Doucet2019, + title = {Abnormal auditory tonotopy in patients with schizophrenia.}, + author = {Doucet, Gaelle E and Luber, Maxwell J and Balchandani, Priti and Sommer, Iris E and Frangou, Sophia}, + journal = {NPJ Schizophr}, + volume = {5}, + number = {1}, + year = {2019}, + month = {Oct}, + pages = {16}, + abstract = {Auditory hallucinations are among the most prevalent and most distressing symptoms of schizophrenia. Despite significant progress, it is still unclear whether auditory hallucinations arise from abnormalities in primary sensory processing or whether they represent failures of higher-order functions. To address this knowledge gap, we capitalized on the increased spatial resolution afforded by ultra-high field imaging at 7 Tesla to investigate the tonotopic organization of the auditory cortex in patients with schizophrenia with a history of recurrent hallucinations. Tonotopy is a fundamental feature of the functional organization of the auditory cortex that is established very early in development and predates the onset of symptoms by decades. Compared to healthy participants, patients showed abnormally increased activation and altered tonotopic organization of the auditory cortex during a purely perceptual task, which involved passive listening to tones across a range of frequencies (88-8000 Hz). These findings suggest that the predisposition to auditory hallucinations is likely to be predicated on abnormalities in the functional organization of the auditory cortex and which may serve as a biomarker for the early identification of vulnerable individuals.}, + pubmed = {31578332}, + doi = {10.1038/s41537-019-0084-x}, + pii = {10.1038/s41537-019-0084-x}, + pmc = {PMC6775081}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/31578332}, + file = {papers/Doucet_NPJSchizophr2019-31578332.pdf}, + nlmuniqueid = {101657919} +} + +@article{Rudy2011, + title = {Three groups of interneurons account for nearly 100% of neocortical GABAergic neurons.}, + author = {Rudy, Bernardo and Fishell, Gordon and Lee, SooHyun and Hjerling-Leffler, Jens}, + journal = {Dev Neurobiol}, + volume = {71}, + number = {1}, + year = {2011}, + month = {Jan}, + pages = {45-61}, + abstract = {An understanding of the diversity of cortical GABAergic interneurons is critical to understand the function of the cerebral cortex. Recent data suggest that neurons expressing three markers, the Ca2+-binding protein parvalbumin (PV), the neuropeptide somatostatin (SST), and the ionotropic serotonin receptor 5HT3a (5HT3aR) account for nearly 100% of neocortical interneurons. Interneurons expressing each of these markers have a different embryological origin. Each group includes several types of interneurons that differ in morphological and electrophysiological properties and likely have different functions in the cortical circuit. The PV group accounts for ∼40% of GABAergic neurons and includes fast spiking basket cells and chandelier cells. The SST group, which represents ∼30% of GABAergic neurons, includes the Martinotti cells and a set of neurons that specifically target layerIV. The 5HT3aR group, which also accounts for ∼30% of the total interneuronal population, is heterogeneous and includes all of the neurons that express the neuropeptide VIP, as well as an equally numerous subgroup of neurons that do not express VIP and includes neurogliaform cells. The universal modulation of these neurons by serotonin and acetylcholine via ionotropic receptors suggests that they might be involved in shaping cortical circuits during specific brain states and behavioral contexts.}, + pubmed = {21154909}, + doi = {10.1002/dneu.20853}, + pmc = {PMC3556905}, + mid = {NIHMS434044}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/21154909}, + file = {papers/Rudy_DevNeurobiol2011-21154909.pdf}, + nlmuniqueid = {101300215} +} + +@article{Athilingam2017, + title = {Serotonin enhances excitability and gamma frequency temporal integration in mouse prefrontal fast-spiking interneurons.}, + author = {Athilingam, Jegath C and Ben-Shalom, Roy and Keeshen, Caroline M and Sohal, Vikaas S and Bender, Kevin J}, + journal = {Elife}, + volume = {6}, + year = {2017}, + month = {12}, + pages = {}, + abstract = {The medial prefrontal cortex plays a key role in higher order cognitive functions like decision making and social cognition. These complex behaviors emerge from the coordinated firing of prefrontal neurons. Fast-spiking interneurons (FSIs) control the timing of excitatory neuron firing via somatic inhibition and generate gamma (30-100 Hz) oscillations. Therefore, factors that regulate how FSIs respond to gamma-frequency input could affect both prefrontal circuit activity and behavior. Here, we show that serotonin (5HT), which is known to regulate gamma power, acts via 5HT2A receptors to suppress an inward-rectifying potassium conductance in FSIs. This leads to depolarization, increased input resistance, enhanced spiking, and slowed decay of excitatory post-synaptic potentials (EPSPs). Notably, we found that slowed EPSP decay preferentially enhanced temporal summation and firing elicited by gamma frequency inputs. These findings show how changes in passive membrane properties can affect not only neuronal excitability but also the temporal filtering of synaptic inputs.}, + keywords = {fast-spiking interneurons; mouse; neuroscience; parvalbumin interneurons; prefrontal cortex; serotonin; synaptic integration; temporal summation; Action Potentials; Animals; Electric Conductivity; Gamma Rhythm; Interneurons; Mice; Models, Neurological; Optical Imaging; Potassium Channels; Prefrontal Cortex; Receptors, Serotonin; Serotonin; }, + pubmed = {29206101}, + doi = {10.7554/eLife.31991}, + pmc = {PMC5746342}, + pii = {31991}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/29206101}, + file = {}, + nlmuniqueid = {101579614} +} + +@article{Weber2010, + title = {Htr2a Gene and 5-HT(2A) Receptor Expression in the Cerebral Cortex Studied Using Genetically Modified Mice.}, + author = {Weber, Elaine T and Andrade, Rodrigo}, + journal = {Front Neurosci}, + volume = {4}, + year = {2010}, + pages = {}, + abstract = {Serotonin receptors of the 5-HT(2A) subtype are robustly expressed in the cerebral cortex where they have been implicated in the pathophysiology and therapeutics of mental disorders and the actions of hallucinogens. Much less is known, however, about the specific cell types expressing 5-HT(2A) receptors in cortex. In the current study we use immunohistochemical and electrophysiological approaches in genetically modified mice to address the expression of the Htr2a gene and 5-HT(2A) receptors in cortex. We first use an EGFP-expressing BAC transgenic mice and identify three main Htr2A gene expressing neuronal populations in cortex. The largest of these cell populations corresponds to layer V pyramidal cells of the anterior cortex, followed by GABAergic interneurons of the middle layers, and non-pyramidal cells of the subplate/Layer VIb. We then use 5-HT(2A) receptor knockout mice to identify an antibody capable of localizing 5-HT(2A) receptors in brain and use it to map these receptors. We find strong laminar expression of 5-HT(2A) receptors in cortex, especially along a diffuse band overlaying layer Va. This band exhibits a strong anteroposterior gradient that closely matches the localization of Htr2A expressing pyramidal cells of layer V. Finally we use electrophysiological and immunohistochemical approaches to show that most, but not all, GABAergic interneurons of the middle layers are parvalbumin expressing Fast-spiking interneurons and that these cells are depolarized and excited by serotonin, most likely through the activation of 5-HT(2A) receptors. These results clarify and extend our understanding of the cellular distribution of 5-HT(2A) receptors in the cerebral cortex.}, + keywords = {5-HT2A; cortex; interneuron; prefrontal; pyramidal cell; serotonin; serotonin receptors; }, + pubmed = {20802802}, + doi = {10.3389/fnins.2010.00036}, + pmc = {PMC2928707}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/20802802}, + file = {}, + nlmuniqueid = {101478481} +} + +@article{Nichols2016, + title = {Psychedelics.}, + author = {Nichols, David E}, + journal = {Pharmacol Rev}, + volume = {68}, + number = {2}, + year = {2016}, + month = {Apr}, + pages = {264-355}, + abstract = {Psychedelics (serotonergic hallucinogens) are powerful psychoactive substances that alter perception and mood and affect numerous cognitive processes. They are generally considered physiologically safe and do not lead to dependence or addiction. Their origin predates written history, and they were employed by early cultures in many sociocultural and ritual contexts. After the virtually contemporaneous discovery of (5R,8R)-(+)-lysergic acid-N,N-diethylamide (LSD)-25 and the identification of serotonin in the brain, early research focused intensively on the possibility that LSD and other psychedelics had a serotonergic basis for their action. Today there is a consensus that psychedelics are agonists or partial agonists at brain serotonin 5-hydroxytryptamine 2A receptors, with particular importance on those expressed on apical dendrites of neocortical pyramidal cells in layer V. Several useful rodent models have been developed over the years to help unravel the neurochemical correlates of serotonin 5-hydroxytryptamine 2A receptor activation in the brain, and a variety of imaging techniques have been employed to identify key brain areas that are directly affected by psychedelics. Recent and exciting developments in the field have occurred in clinical research, where several double-blind placebo-controlled phase 2 studies of psilocybin-assisted psychotherapy in patients with cancer-related psychosocial distress have demonstrated unprecedented positive relief of anxiety and depression. Two small pilot studies of psilocybin-assisted psychotherapy also have shown positive benefit in treating both alcohol and nicotine addiction. Recently, blood oxygen level-dependent functional magnetic resonance imaging and magnetoencephalography have been employed for in vivo brain imaging in humans after administration of a psychedelic, and results indicate that intravenously administered psilocybin and LSD produce decreases in oscillatory power in areas of the brain's default mode network. }, + pubmed = {26841800}, + pii = {68/2/264}, + doi = {10.1124/pr.115.011478}, + pmc = {PMC4813425}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/26841800}, + file = {papers/Nichols_PharmacolRev2016-26841800.pdf}, + nlmuniqueid = {0421737} +} + +@article{Kvam2018, + title = {Psychedelic drugs in the treatment of anxiety, depression and addiction.}, + author = {Kvam, Tor-Morten and Stewart, Lowan H and Andreassen, Ole A}, + journal = {Tidsskr Nor Laegeforen}, + volume = {138}, + number = {18}, + year = {2018}, + month = {11}, + pages = {}, + abstract = {Det er økt interesse for psykedeliske stoffer til bruk i behandling av psykiske lidelser. Stoffene regnes som trygge når de gis innenfor en klinisk ramme. Eldre studier fra før 1970 har metodologiske svakheter, men i de senere år har det kommet lovende resultater fra bruk ved unipolar depresjon, depresjon ved livstruende sykdom, angst og avhengighet. Formålet med denne litteraturgjennomgangen er å gi en oversikt over nyere resultater og disse studienes begrensninger.}, + pubmed = {30421744}, + pii = {17-1110}, + doi = {10.4045/tidsskr.17.1110}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/30421744}, + file = {papers/Kvam_TidsskrNorLaegeforen2018-30421744.pdf}, + nlmuniqueid = {0413423} +} + +@article{Carhart-Harris2014, + title = {The entropic brain: a theory of conscious states informed by neuroimaging research with psychedelic drugs.}, + author = {Carhart-Harris, Robin L and Leech, Robert and Hellyer, Peter J and Shanahan, Murray and Feilding, Amanda and Tagliazucchi, Enzo and Chialvo, Dante R and Nutt, David}, + journal = {Front Hum Neurosci}, + volume = {8}, + year = {2014}, + pages = {20}, + abstract = {Entropy is a dimensionless quantity that is used for measuring uncertainty about the state of a system but it can also imply physical qualities, where high entropy is synonymous with high disorder. Entropy is applied here in the context of states of consciousness and their associated neurodynamics, with a particular focus on the psychedelic state. The psychedelic state is considered an exemplar of a primitive or primary state of consciousness that preceded the development of modern, adult, human, normal waking consciousness. Based on neuroimaging data with psilocybin, a classic psychedelic drug, it is argued that the defining feature of "primary states" is elevated entropy in certain aspects of brain function, such as the repertoire of functional connectivity motifs that form and fragment across time. Indeed, since there is a greater repertoire of connectivity motifs in the psychedelic state than in normal waking consciousness, this implies that primary states may exhibit "criticality," i.e., the property of being poised at a "critical" point in a transition zone between order and disorder where certain phenomena such as power-law scaling appear. Moreover, if primary states are critical, then this suggests that entropy is suppressed in normal waking consciousness, meaning that the brain operates just below criticality. It is argued that this entropy suppression furnishes normal waking consciousness with a constrained quality and associated metacognitive functions, including reality-testing and self-awareness. It is also proposed that entry into primary states depends on a collapse of the normally highly organized activity within the default-mode network (DMN) and a decoupling between the DMN and the medial temporal lobes (which are normally significantly coupled). These hypotheses can be tested by examining brain activity and associated cognition in other candidate primary states such as rapid eye movement (REM) sleep and early psychosis and comparing these with non-primary states such as normal waking consciousness and the anaesthetized state. }, + keywords = {5-HT2A receptor; REM sleep; consciousness; criticality; default mode network; entropy; metastability; serotonin; }, + pubmed = {24550805}, + doi = {10.3389/fnhum.2014.00020}, + pmc = {PMC3909994}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/24550805}, + file = {papers/Carhart-Harris_FrontHumNeurosci2014-24550805.pdf}, + nlmuniqueid = {101477954} +} + +@article{Tononi1994, + title = {A measure for brain complexity: relating functional segregation and integration in the nervous system.}, + author = {Tononi, G and Sporns, O and Edelman, G M}, + journal = {Proc Natl Acad Sci U S A}, + volume = {91}, + number = {11}, + year = {1994}, + month = {May}, + pages = {5033-7}, + abstract = {In brains of higher vertebrates, the functional segregation of local areas that differ in their anatomy and physiology contrasts sharply with their global integration during perception and behavior. In this paper, we introduce a measure, called neural complexity (CN), that captures the interplay between these two fundamental aspects of brain organization. We express functional segregation within a neural system in terms of the relative statistical independence of small subsets of the system and functional integration in terms of significant deviations from independence of large subsets. CN is then obtained from estimates of the average deviation from statistical independence for subsets of increasing size. CN is shown to be high when functional segregation coexists with integration and to be low when the components of a system are either completely independent (segregated) or completely dependent (integrated). We apply this complexity measure in computer simulations of cortical areas to examine how some basic principles of neuroanatomical organization constrain brain dynamics. We show that the connectivity patterns of the cerebral cortex, such as a high density of connections, strong local connectivity organizing cells into neuronal groups, patchiness in the connectivity among neuronal groups, and prevalent reciprocal connections, are associated with high values of CN. The approach outlined here may prove useful in analyzing complexity in other biological domains such as gene regulation and embryogenesis.}, + pubmed = {8197179}, + pmc = {PMC43925}, + doi = {10.1073/pnas.91.11.5033}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/8197179}, + file = {papers/Tononi_ProcNatlAcadSciUSA1994-8197179.pdf}, + nlmuniqueid = {7505876} +} + +@article{Ly2018, + title = {Psychedelics Promote Structural and Functional Neural Plasticity.}, + author = {Ly, Calvin and Greb, Alexandra C and Cameron, Lindsay P and Wong, Jonathan M and Barragan, Eden V and Wilson, Paige C and Burbach, Kyle F and Soltanzadeh Zarandi, Sina and Sood, Alexander and Paddy, Michael R and Duim, Whitney C and Dennis, Megan Y and McAllister, A Kimberley and Ori-McKenney, Kassandra M and Gray, John A and Olson, David E}, + journal = {Cell Rep}, + volume = {23}, + number = {11}, + year = {2018}, + month = {06}, + pages = {3170-3182}, + abstract = {Atrophy of neurons in the prefrontal cortex (PFC) plays a key role in the pathophysiology of depression and related disorders. The ability to promote both structural and functional plasticity in the PFC has been hypothesized to underlie the fast-acting antidepressant properties of the dissociative anesthetic ketamine. Here, we report that, like ketamine, serotonergic psychedelics are capable of robustly increasing neuritogenesis and/or spinogenesis both in vitro and in vivo. These changes in neuronal structure are accompanied by increased synapse number and function, as measured by fluorescence microscopy and electrophysiology. The structural changes induced by psychedelics appear to result from stimulation of the TrkB, mTOR, and 5-HT2A signaling pathways and could possibly explain the clinical effectiveness of these compounds. Our results underscore the therapeutic potential of psychedelics and, importantly, identify several lead scaffolds for medicinal chemistry efforts focused on developing plasticity-promoting compounds as safe, effective, and fast-acting treatments for depression and related disorders.}, + keywords = {DMT; LSD; MDMA; depression; ketamine; neural plasticity; noribogaine; psychedelic; spinogenesis; synaptogenesis; Animals; Antidepressive Agents; Brain-Derived Neurotrophic Factor; Cells, Cultured; Cerebral Cortex; Female; Male; Microscopy, Fluorescence; Neurogenesis; Neuronal Plasticity; Rats; Rats, Sprague-Dawley; Receptor, Serotonin, 5-HT2A; Receptor, trkB; Signal Transduction; TOR Serine-Threonine Kinases; }, + pubmed = {29898390}, + pii = {S2211-1247(18)30755-1}, + doi = {10.1016/j.celrep.2018.05.022}, + pmc = {PMC6082376}, + mid = {NIHMS977843}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/29898390}, + file = {papers/Ly_CellRep2018-29898390.pdf}, + nlmuniqueid = {101573691} +} + +@article{Wasko2018, + title = {DARK Classics in Chemical Neuroscience: Ibogaine.}, + author = {Wasko, Michael J and Witt-Enderby, Paula A and Surratt, Christopher K}, + journal = {ACS Chem Neurosci}, + volume = {9}, + number = {10}, + year = {2018}, + month = {10}, + pages = {2475-2483}, + abstract = {The West African iboga plant has been used for centuries by the Bwiti and Mbiri tribes to induce hallucinations during religious ceremonies. Ibogaine, the principal alkaloid responsible for iboga's psychedelic properties, was isolated and sold as an antidepressant in France for decades before its adverse effects precipitated its removal from the market. An ibogaine resurgence in the 1960s was driven by U.S. heroin addicts who claimed that ibogaine cured their opiate addictions. Behavioral pharmacologic studies in animal models provided evidence that ibogaine could blunt self-administration of not only opiates but cocaine, amphetamines, and nicotine. Ibogaine displays moderate-to-weak affinities for a wide spectrum of receptor and transporter proteins; recent work suggests that its actions at nicotinic acetylcholine receptor subtypes may underlie its reputed antiopiate effects. At micromolar levels, ibogaine is neurotoxic and cardiotoxic and has been linked to several deaths by cardiac arrest. Structure-activity studies led to the isolation of the ibogaine analog 18-methoxycoronaridine (18-MC), an α3β4 nicotinic receptor modulator that retains ibogaine's anticraving properties with few or no adverse effects. Clinical trials of 18-MC treatment of nicotine addiction are pending. Ibogaine analogs may also hold promise for treating anxiety and depression via the "psychedelic-assisted therapy" approach that employs hallucinogens including psilocybin and methylenedioxymethamphetamine ("ecstasy").}, + keywords = {addiction; hallucinogen; iboga; nicotine; opioid; therapeutic; Cardiotoxicity; Hallucinogens; History, 20th Century; History, 21st Century; Humans; Ibogaine; Receptors, Nicotinic; Structure-Activity Relationship; Substance-Related Disorders; Tabernaemontana; }, + pubmed = {30216039}, + doi = {10.1021/acschemneuro.8b00294}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/30216039}, + file = {papers/Wasko_ACSChemNeurosci2018-30216039.pdf}, + nlmuniqueid = {101525337} +} + +@article{Alper2012, + title = {Fatalities temporally associated with the ingestion of ibogaine.}, + author = {Alper, Kenneth R and Stajić, Marina and Gill, James R}, + journal = {J Forensic Sci}, + volume = {57}, + number = {2}, + year = {2012}, + month = {Mar}, + pages = {398-412}, + abstract = {Ibogaine is a naturally occurring psychoactive plant alkaloid that is used globally in medical and nonmedical settings for opioid detoxification and other substance use indications. All available autopsy, toxicological, and investigative reports were systematically reviewed for the consecutive series of all known fatalities outside of West Central Africa temporally related to the use of ibogaine from 1990 through 2008. Nineteen individuals (15 men, four women between 24 and 54 years old) are known to have died within 1.5-76 h of taking ibogaine. The clinical and postmortem evidence did not suggest a characteristic syndrome of neurotoxicity. Advanced preexisting medical comorbidities, which were mainly cardiovascular, and/or one or more commonly abused substances explained or contributed to the death in 12 of the 14 cases for which adequate postmortem data were available. Other apparent risk factors include seizures associated with withdrawal from alcohol and benzodiazepines and the uninformed use of ethnopharmacological forms of ibogaine.}, + pubmed = {22268458}, + doi = {10.1111/j.1556-4029.2011.02008.x}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/22268458}, + file = {papers/Alper_JForensicSci2012-22268458.pdf}, + nlmuniqueid = {0375370} +} + +@article{Raouf2017, + title = {Serotonin-norepinephrine reuptake inhibitors and the influence of binding affinity (Ki) on analgesia.}, + author = {Raouf, M and Glogowski, A J and Bettinger, J J and Fudin, J}, + journal = {J Clin Pharm Ther}, + volume = {42}, + number = {4}, + year = {2017}, + month = {Aug}, + pages = {513-517}, + abstract = {Serotonin-norepinephrine reuptake inhibitors (SNRIs) are commonly used for various psychiatric conditions and neuropathic pain syndromes. SNRIs inhibit the reuptake of serotonin (5-HT) and norepinephrine (NE); however, NE reuptake inhibition is thought to be the primary mediator for their analgesic effect.}, + keywords = {antidepressants; binding affinity; neuropathic pain; pain; serotonin-norepinephrine reuptake inhibitors; Analgesics; Dose-Response Relationship, Drug; Humans; Neuralgia; Norepinephrine; Serotonin; Serotonin and Noradrenaline Reuptake Inhibitors; }, + pubmed = {28503727}, + doi = {10.1111/jcpt.12534}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/28503727}, + file = {papers/Raouf_JClinPharmTher2017-28503727.pdf}, + nlmuniqueid = {8704308} +} + +@article{Bymaster2001, + title = {Comparative affinity of duloxetine and venlafaxine for serotonin and norepinephrine transporters in vitro and in vivo, human serotonin receptor subtypes, and other neuronal receptors.}, + author = {Bymaster, F P and Dreshfield-Ahmad, L J and Threlkeld, P G and Shaw, J L and Thompson, L and Nelson, D L and Hemrick-Luecke, S K and Wong, D T}, + journal = {Neuropsychopharmacology}, + volume = {25}, + number = {6}, + year = {2001}, + month = {Dec}, + pages = {871-80}, + abstract = {The blockade of serotonin (5-HT) and norepinephrine (NE) transporters in vitro and in vivo by the dual 5-HT/NE reuptake inhibitors duloxetine and venlafaxine was compared. Duloxetine inhibited binding to the human NE and 5-HT transporters with K(i) values of 7.5 and 0.8 nM, respectively, and with a K(i) ratio of 9. Venlafaxine inhibited binding to the human NE and 5-HT transporters with K(i) values of 2480 and 82 nM, respectively, and with a K(i) ratio of 30. Duloxetine inhibited ex vivo binding to rat 5-HT transporters and NE transporters with ED(50) values of 0.03 and 0.7 mg/kg, respectively, whereas venlafaxine had ED(50) values of 2 and 54 mg/kg, respectively. The depletion of rat brain 5-HT by p-chloramphetamine and depletion of rat hypothalamic NE by 6-hydroxydopamine was blocked by duloxetine with ED(50) values of 2.3 and 12 mg/kg, respectively. Venlafaxine had ED(50) values of 5.9 and 94 mg/kg for blocking p-chloramphetamine- and 6-hydroxydopamine-induced monoamine depletion, respectively. Thus, duloxetine more potently blocks 5-HT and NE transporters in vitro and in vivo than venlafaxine.}, + pubmed = {11750180}, + pii = {S0893133X01002986}, + doi = {10.1016/S0893-133X(01)00298-6}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/11750180}, + file = {papers/Bymaster_Neuropsychopharmacology2001-11750180.pdf}, + nlmuniqueid = {8904907} +} + +@article{Ray2010, + title = {Psychedelics and the human receptorome.}, + author = {Ray, Thomas S}, + journal = {PLoS One}, + volume = {5}, + number = {2}, + year = {2010}, + month = {Feb}, + pages = {e9019}, + abstract = {We currently understand the mental effects of psychedelics to be caused by agonism or partial agonism of 5-HT(2A) (and possibly 5-HT(2C)) receptors, and we understand that psychedelic drugs, especially phenylalkylamines, are fairly selective for these two receptors. This manuscript is a reference work on the receptor affinity pharmacology of psychedelic drugs. New data is presented on the affinity of twenty-five psychedelic drugs at fifty-one receptors, transporters, and ion channels, assayed by the National Institute of Mental Health-Psychoactive Drug Screening Program (NIMH-PDSP). In addition, comparable data gathered from the literature on ten additional drugs is also presented (mostly assayed by the NIMH-PDSP). A new method is introduced for normalizing affinity (K(i)) data that factors out potency so that the multi-receptor affinity profiles of different drugs can be directly compared and contrasted. The method is then used to compare the thirty-five drugs in graphical and tabular form. It is shown that psychedelic drugs, especially phenylalkylamines, are not as selective as generally believed, interacting with forty-two of forty-nine broadly assayed sites. The thirty-five drugs of the study have very diverse patterns of interaction with different classes of receptors, emphasizing eighteen different receptors. This diversity of receptor interaction may underlie the qualitative diversity of these drugs. It should be possible to use this diverse set of drugs as probes into the roles played by the various receptor systems in the human mind.}, + pubmed = {20126400}, + doi = {10.1371/journal.pone.0009019}, + pmc = {PMC2814854}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/20126400}, + file = {papers/Ray_PLoSOne2010-20126400.pdf}, + nlmuniqueid = {101285081} +} + +@article{Orsolini2017, + title = {The "Endless Trip" among the NPS Users: Psychopathology and Psychopharmacology in the Hallucinogen-Persisting Perception Disorder. A Systematic Review.}, + author = {Orsolini, Laura and Papanti, Gabriele Duccio and De Berardis, Domenico and Guirguis, Amira and Corkery, John Martin and Schifano, Fabrizio}, + journal = {Front Psychiatry}, + volume = {8}, + year = {2017}, + pages = {240}, + abstract = {Hallucinogen-persisting perception disorder (HPPD) is a syndrome characterized by prolonged or reoccurring perceptual symptoms, reminiscent of acute hallucinogen effects. HPPD was associated with a broader range of LSD (lysergic acid diethylamide)-like substances, cannabis, methylenedioxymethamphetamine (MDMA), psilocybin, mescaline, and psychostimulants. The recent emergence of novel psychoactive substances (NPS) posed a critical concern regarding the new onset of psychiatric symptoms/syndromes, including cases of HPPD. Symptomatology mainly comprises visual disorders (i.e., geometric pseudo-hallucinations, haloes, flashes of colors/lights, motion-perception deficits, afterimages, micropsia, more acute awareness of floaters, etc.), even though depressive symptoms and thought disorders may be comorbidly present. Although HPPD was first described in 1954, it was just established as a fully syndrome in 2000, with the revised fourth version of the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV-TR). HPPD neural substrates, risk factors, and aetiopathogenesys still largely remain unknown and under investigation, and many questions about its pharmacological targets remain unanswered too. A critical mini review on psychopathological bases, etiological hypothesis, and psychopharmacological approaches toward HPPD, including the association with some novel substances, are provided here, by means of a literature search on PubMed/Medline, Google Scholar, and Scopus databases without time restrictions, by using a specific set of keywords. Pharmacological and clinical issues are considered, and practical psychopharmacological recommendations and clinical guidelines are suggested.}, + keywords = {flashbacks; hallucinations; hallucinogen-persisting perception disorder; hallucinogens; novel psychoactive substances; palinopsia; }, + pubmed = {29209235}, + doi = {10.3389/fpsyt.2017.00240}, + pmc = {PMC5701998}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/29209235}, + file = {papers/Orsolini_FrontPsychiatry2017-29209235.pdf}, + nlmuniqueid = {101545006} +} + +@article{Carhart-Harris2017, + title = {The Therapeutic Potential of Psychedelic Drugs: Past, Present, and Future.}, + author = {Carhart-Harris, Robin L and Goodwin, Guy M}, + journal = {Neuropsychopharmacology}, + volume = {42}, + number = {11}, + year = {2017}, + month = {Oct}, + pages = {2105-2113}, + abstract = {Plant-based psychedelics, such as psilocybin, have an ancient history of medicinal use. After the first English language report on LSD in 1950, psychedelics enjoyed a short-lived relationship with psychology and psychiatry. Used most notably as aids to psychotherapy for the treatment of mood disorders and alcohol dependence, drugs such as LSD showed initial therapeutic promise before prohibitive legislature in the mid-1960s effectively ended all major psychedelic research programs. Since the early 1990s, there has been a steady revival of human psychedelic research: last year saw reports on the first modern brain imaging study with LSD and three separate clinical trials of psilocybin for depressive symptoms. In this circumspective piece, RLC-H and GMG share their opinions on the promises and pitfalls of renewed psychedelic research, with a focus on the development of psilocybin as a treatment for depression.}, + pubmed = {28443617}, + pii = {npp201784}, + doi = {10.1038/npp.2017.84}, + pmc = {PMC5603818}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/28443617}, + file = {papers/Carhart-Harris_Neuropsychopharmacology2017-28443617.pdf}, + nlmuniqueid = {8904907} +} + +@article{Schenberg2018, + title = {Psychedelic-Assisted Psychotherapy: A Paradigm Shift in Psychiatric Research and Development.}, + author = {Schenberg, Eduardo Ekman}, + journal = {Front Pharmacol}, + volume = {9}, + year = {2018}, + pages = {733}, + abstract = {Mental disorders are rising while development of novel psychiatric medications is declining. This stall in innovation has also been linked with intense debates on the current diagnostics and explanations for mental disorders, together constituting a paradigmatic crisis. A radical innovation is psychedelic-assisted psychotherapy (PAP): professionally supervised use of ketamine, MDMA, psilocybin, LSD and ibogaine as part of elaborated psychotherapy programs. Clinical results so far have shown safety and efficacy, even for "treatment resistant" conditions, and thus deserve increasing attention from medical, psychological and psychiatric professionals. But more than novel treatments, the PAP model also has important consequences for the diagnostics and explanation axis of the psychiatric crisis, challenging the discrete nosological entities and advancing novel explanations for mental disorders and their treatment, in a model considerate of social and cultural factors, including adversities, trauma, and the therapeutic potential of some non-ordinary states of consciousness.}, + keywords = {LSD; MDMA; explanation in neuroscience; ibogaine; ketamine; psilocybin; psychedelic-assisted psychotherapy; states of consciousness; }, + pubmed = {30026698}, + doi = {10.3389/fphar.2018.00733}, + pmc = {PMC6041963}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/30026698}, + file = {papers/Schenberg_FrontPharmacol2018-30026698.pdf}, + nlmuniqueid = {101548923} +} + +@article{Roseman2017, + title = {Quality of Acute Psychedelic Experience Predicts Therapeutic Efficacy of Psilocybin for Treatment-Resistant Depression.}, + author = {Roseman, Leor and Nutt, David J and Carhart-Harris, Robin L}, + journal = {Front Pharmacol}, + volume = {8}, + year = {2017}, + pages = {974}, + abstract = {Introduction: It is a basic principle of the "psychedelic" treatment model that the quality of the acute experience mediates long-term improvements in mental health. In the present paper we sought to test this using data from a clinical trial assessing psilocybin for treatment-resistant depression (TRD). In line with previous reports, we hypothesized that the occurrence and magnitude of Oceanic Boundlessness (OBN) (sharing features with mystical-type experience) and Dread of Ego Dissolution (DED) (similar to anxiety) would predict long-term positive outcomes, whereas sensory perceptual effects would have negligible predictive value. Materials and Methods: Twenty patients with treatment resistant depression underwent treatment with psilocybin (two separate sessions: 10 and 25 mg psilocybin). The Altered States of Consciousness (ASC) questionnaire was used to assess the quality of experiences in the 25 mg psilocybin session. From the ASC, the dimensions OBN and DED were used to measure the mystical-type and challenging experiences, respectively. The Self-Reported Quick Inventory of Depressive Symptoms (QIDS-SR) at 5 weeks served as the endpoint clinical outcome measure, as in later time points some of the subjects had gone on to receive new treatments, thus confounding inferences. In a repeated measure ANOVA, Time was the within-subject factor (independent variable), with QIDS-SR as the within-subject dependent variable in baseline, 1-day, 1-week, 5-weeks. OBN and DED were independent variables. OBN-by-Time and DED-by-Time interactions were the primary outcomes of interest. Results: For the interaction of OBN and DED with Time (QIDS-SR as dependent variable), the main effect and the effects at each time point compared to baseline were all significant (p = 0.002 and p = 0.003, respectively, for main effects), confirming our main hypothesis. Furthermore, Pearson's correlation of OBN with QIDS-SR (5 weeks) was specific compared to perceptual dimensions of the ASC (p < 0.05). Discussion: This report further bolsters the view that the quality of the acute psychedelic experience is a key mediator of long-term changes in mental health. Future therapeutic work with psychedelics should recognize the essential importance of quality of experience in determining treatment efficacy and consider ways of enhancing mystical-type experiences and reducing anxiety. Trial Registration: ISRCTN, number ISRCTN14426797, http://www.isrctn.com/ISRCTN14426797.}, + keywords = {depression; mystical experience; peak experience; psilocybin; psychedelics; serotonin; therapy; }, + pubmed = {29387009}, + doi = {10.3389/fphar.2017.00974}, + pmc = {PMC5776504}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/29387009}, + file = {papers/Roseman_FrontPharmacol2017-29387009.pdf}, + nlmuniqueid = {101548923} +} + +@article{Koenig2015, + title = {The anti-addiction drug ibogaine and the heart: a delicate relation.}, + author = {Koenig, Xaver and Hilber, Karlheinz}, + journal = {Molecules}, + volume = {20}, + number = {2}, + year = {2015}, + month = {Jan}, + pages = {2208-28}, + abstract = {The plant indole alkaloid ibogaine has shown promising anti-addictive properties in animal studies. Ibogaine is also anti-addictive in humans as the drug alleviates drug craving and impedes relapse of drug use. Although not licensed as therapeutic drug and despite safety concerns, ibogaine is currently used as an anti-addiction medication in alternative medicine in dozens of clinics worldwide. In recent years, alarming reports of life-threatening complications and sudden death cases, temporally associated with the administration of ibogaine, have been accumulating. These adverse reactions were hypothesised to be associated with ibogaine's propensity to induce cardiac arrhythmias. The aim of this review is to recapitulate the current knowledge about ibogaine's effects on the heart and the cardiovascular system, and to assess the cardiac risks associated with the use of this drug in anti- addiction therapy. The actions of 18-methoxycoronaridine (18-MC), a less toxic ibogaine congener with anti-addictive properties, are also considered. }, + pubmed = {25642835}, + pii = {molecules20022208}, + doi = {10.3390/molecules20022208}, + pmc = {PMC4382526}, + mid = {EMS62840}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/25642835}, + file = {papers/Koenig_Molecules2015-25642835.pdf}, + nlmuniqueid = {100964009} +} + +@article{Saxena2020, + title = {Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data.}, + author = {Saxena, Shreya and Kinsella, Ian and Musall, Simon and Kim, Sharon H and Meszaros, Jozsef and Thibodeaux, David N and Kim, Carla and Cunningham, John and Hillman, Elizabeth M C and Churchland, Anne and Paninski, Liam}, + journal = {PLoS Comput Biol}, + volume = {16}, + number = {4}, + year = {2020}, + month = {04}, + pages = {e1007791}, + abstract = {Widefield calcium imaging enables recording of large-scale neural activity across the mouse dorsal cortex. In order to examine the relationship of these neural signals to the resulting behavior, it is critical to demix the recordings into meaningful spatial and temporal components that can be mapped onto well-defined brain regions. However, no current tools satisfactorily extract the activity of the different brain regions in individual mice in a data-driven manner, while taking into account mouse-specific and preparation-specific differences. Here, we introduce Localized semi-Nonnegative Matrix Factorization (LocaNMF), a method that efficiently decomposes widefield video data and allows us to directly compare activity across multiple mice by outputting mouse-specific localized functional regions that are significantly more interpretable than more traditional decomposition techniques. Moreover, it provides a natural subspace to directly compare correlation maps and neural dynamics across different behaviors, mice, and experimental conditions, and enables identification of task- and movement-related brain regions.}, + pubmed = {32282806}, + doi = {10.1371/journal.pcbi.1007791}, + pii = {PCOMPBIOL-D-19-01682}, + pmc = {PMC7179949}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/32282806}, + file = {papers/Saxena_PLoSComputBiol2020-32282806.pdf}, + nlmuniqueid = {101238922} +} + +@article{Botvinik-Nezer2020, + title = {Variability in the analysis of a single neuroimaging dataset by many teams.}, + author = {Botvinik-Nezer, Rotem and Holzmeister, Felix and Camerer, Colin F and Dreber, Anna and Huber, Juergen and Johannesson, Magnus and Kirchler, Michael and Iwanir, Roni and Mumford, Jeanette A and Adcock, R Alison and Avesani, Paolo and Baczkowski, Blazej M and Bajracharya, Aahana and Bakst, Leah and Ball, Sheryl and Barilari, Marco and Bault, Nadège and Beaton, Derek and Beitner, Julia and Benoit, Roland G and Berkers, Ruud M W J and Bhanji, Jamil P and Biswal, Bharat B and Bobadilla-Suarez, Sebastian and Bortolini, Tiago and Bottenhorn, Katherine L and Bowring, Alexander and Braem, Senne and Brooks, Hayley R and Brudner, Emily G and Calderon, Cristian B and Camilleri, Julia A and Castrellon, Jaime J and Cecchetti, Luca and Cieslik, Edna C and Cole, Zachary J and Collignon, Olivier and Cox, Robert W and Cunningham, William A and Czoschke, Stefan and Dadi, Kamalaker and Davis, Charles P and Luca, Alberto De and Delgado, Mauricio R and Demetriou, Lysia and Dennison, Jeffrey B and Di, Xin and Dickie, Erin W and Dobryakova, Ekaterina and Donnat, Claire L and Dukart, Juergen and Duncan, Niall W and Durnez, Joke and Eed, Amr and Eickhoff, Simon B and Erhart, Andrew and Fontanesi, Laura and Fricke, G Matthew and Fu, Shiguang and Galván, Adriana and Gau, Remi and Genon, Sarah and Glatard, Tristan and Glerean, Enrico and Goeman, Jelle J and Golowin, Sergej A E and González-García, Carlos and Gorgolewski, Krzysztof J and Grady, Cheryl L and Green, Mikella A and Guassi Moreira, João F and Guest, Olivia and Hakimi, Shabnam and Hamilton, J Paul and Hancock, Roeland and Handjaras, Giacomo and Harry, Bronson B and Hawco, Colin and Herholz, Peer and Herman, Gabrielle and Heunis, Stephan and Hoffstaedter, Felix and Hogeveen, Jeremy and Holmes, Susan and Hu, Chuan-Peng and Huettel, Scott A and Hughes, Matthew E and Iacovella, Vittorio and Iordan, Alexandru D and Isager, Peder M and Isik, Ayse I and Jahn, Andrew and Johnson, Matthew R and Johnstone, Tom and Joseph, Michael J E and Juliano, Anthony C and Kable, Joseph W and Kassinopoulos, Michalis and Koba, Cemal and Kong, Xiang-Zhen and Koscik, Timothy R and Kucukboyaci, Nuri Erkut and Kuhl, Brice A and Kupek, Sebastian and Laird, Angela R and Lamm, Claus and Langner, Robert and Lauharatanahirun, Nina and Lee, Hongmi and Lee, Sangil and Leemans, Alexander and Leo, Andrea and Lesage, Elise and Li, Flora and Li, Monica Y C and Lim, Phui Cheng and Lintz, Evan N and Liphardt, Schuyler W and Losecaat Vermeer, Annabel B and Love, Bradley C and Mack, Michael L and Malpica, Norberto and Marins, Theo and Maumet, Camille and McDonald, Kelsey and McGuire, Joseph T and Melero, Helena and Méndez Leal, Adriana S and Meyer, Benjamin and Meyer, Kristin N and Mihai, Glad and Mitsis, Georgios D and Moll, Jorge and Nielson, Dylan M and Nilsonne, Gustav and Notter, Michael P and Olivetti, Emanuele and Onicas, Adrian I and Papale, Paolo and Patil, Kaustubh R and Peelle, Jonathan E and Pérez, Alexandre and Pischedda, Doris and Poline, Jean-Baptiste and Prystauka, Yanina and Ray, Shruti and Reuter-Lorenz, Patricia A and Reynolds, Richard C and Ricciardi, Emiliano and Rieck, Jenny R and Rodriguez-Thompson, Anais M and Romyn, Anthony and Salo, Taylor and Samanez-Larkin, Gregory R and Sanz-Morales, Emilio and Schlichting, Margaret L and Schultz, Douglas H and Shen, Qiang and Sheridan, Margaret A and Silvers, Jennifer A and Skagerlund, Kenny and Smith, Alec and Smith, David V and Sokol-Hessner, Peter and Steinkamp, Simon R and Tashjian, Sarah M and Thirion, Bertrand and Thorp, John N and Tinghög, Gustav and Tisdall, Loreen and Tompson, Steven H and Toro-Serey, Claudio and Torre Tresols, Juan Jesus and Tozzi, Leonardo and Truong, Vuong and Turella, Luca and van 't Veer, Anna E and Verguts, Tom and Vettel, Jean M and Vijayarajah, Sagana and Vo, Khoi and Wall, Matthew B and Weeda, Wouter D and Weis, Susanne and White, David J and Wisniewski, David and Xifra-Porxas, Alba and Yearling, Emily A and Yoon, Sangsuk and Yuan, Rui and Yuen, Kenneth S L and Zhang, Lei and Zhang, Xu and Zosky, Joshua E and Nichols, Thomas E and Poldrack, Russell A and Schonberg, Tom}, + journal = {Nature}, + volume = {582}, + number = {7810}, + year = {2020}, + month = {06}, + pages = {84-88}, + abstract = {Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses1. The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset2-5. Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed.}, + pubmed = {32483374}, + doi = {10.1038/s41586-020-2314-9}, + pii = {10.1038/s41586-020-2314-9}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/32483374}, + file = {papers/Botvinik-Nezer_Nature2020-32483374.pdf}, + nlmuniqueid = {0410462} +} + +@article{VanEssen2012, + title = {Cortical cartography and Caret software.}, + author = {Van Essen, David C}, + journal = {Neuroimage}, + volume = {62}, + number = {2}, + year = {2012}, + month = {Aug}, + pages = {757-64}, + abstract = {Caret software is widely used for analyzing and visualizing many types of fMRI data, often in conjunction with experimental data from other modalities. This article places Caret's development in a historical context that spans three decades of brain mapping--from the early days of manually generated flat maps to the nascent field of human connectomics. It also highlights some of Caret's distinctive capabilities. This includes the ease of visualizing data on surfaces and/or volumes and on atlases as well as individual subjects. Caret can display many types of experimental data using various combinations of overlays (e.g., fMRI activation maps, cortical parcellations, areal boundaries), and it has other features that facilitate the analysis and visualization of complex neuroimaging datasets.}, + pubmed = {22062192}, + pii = {S1053-8119(11)01241-9}, + doi = {10.1016/j.neuroimage.2011.10.077}, + pmc = {PMC3288593}, + mid = {NIHMS335250}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/22062192}, + file = {papers/VanEssen_Neuroimage2012-22062192.pdf}, + nlmuniqueid = {9215515} +} + +@article{Ioannidis2005, + title = {Why most published research findings are false.}, + author = {Ioannidis, John P A}, + journal = {PLoS Med}, + volume = {2}, + number = {8}, + year = {2005}, + month = {Aug}, + pages = {e124}, + abstract = {There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research.}, + pubmed = {16060722}, + pii = {04-PLME-E-0321R2}, + doi = {10.1371/journal.pmed.0020124}, + pmc = {PMC1182327}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/16060722}, + file = {papers/Ioannidis_PLoSMed2005-16060722.pdf}, + nlmuniqueid = {101231360} +} + +@article{Ioannidis2014, + title = {How to make more published research true.}, + author = {Ioannidis, John P A}, + journal = {PLoS Med}, + volume = {11}, + number = {10}, + year = {2014}, + month = {Oct}, + pages = {e1001747}, + abstract = {In a 2005 paper that has been accessed more than a million times, John Ioannidis explained why most published research findings were false. Here he revisits the topic, this time to address how to improve matters. Please see later in the article for the Editors' Summary. }, + pubmed = {25334033}, + doi = {10.1371/journal.pmed.1001747}, + pii = {PMEDICINE-D-14-01145}, + pmc = {PMC4204808}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/25334033}, + file = {papers/Ioannidis_PLoSMed2014-25334033.pdf}, + nlmuniqueid = {101231360} +} + +@article{Barchi1995, + title = {Molecular pathology of the skeletal muscle sodium channel.}, + author = {Barchi, R L}, + journal = {Annu Rev Physiol}, + volume = {57}, + year = {1995}, + pages = {355-85}, + pubmed = {7778872}, + doi = {10.1146/annurev.ph.57.030195.002035}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/7778872}, + file = {papers/Barchi_AnnuRevPhysiol1995-7778872.pdf}, + nlmuniqueid = {0370600} +} + +@article{Hyvarinen2013, + title = {Independent component analysis: recent advances.}, + author = {Hyvärinen, Aapo}, + journal = {Philos Trans A Math Phys Eng Sci}, + volume = {371}, + number = {1984}, + year = {2013}, + month = {Feb}, + pages = {20110534}, + abstract = {Independent component analysis is a probabilistic method for learning a linear transform of a random vector. The goal is to find components that are maximally independent and non-Gaussian (non-normal). Its fundamental difference to classical multi-variate statistical methods is in the assumption of non-Gaussianity, which enables the identification of original, underlying components, in contrast to classical methods. The basic theory of independent component analysis was mainly developed in the 1990s and summarized, for example, in our monograph in 2001. Here, we provide an overview of some recent developments in the theory since the year 2000. The main topics are: analysis of causal relations, testing independent components, analysing multiple datasets (three-way data), modelling dependencies between the components and improved methods for estimating the basic model.}, + pubmed = {23277597}, + pii = {rsta.2011.0534}, + doi = {10.1098/rsta.2011.0534}, + pmc = {PMC3538438}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/23277597}, + file = {papers/Hyvärinen_PhilosTransAMathPhysEngSci2013-23277597.pdf}, + nlmuniqueid = {101133385} +} + +@article{Hyvarinen2016, + author = {Hyvärinen, Aapo and Morioka, Hiroshi}, + title = {Unsupervised Feature Extraction by Time-Contrastive Learning and Nonlinear ICA}, + journal = {arXiv}, + year = {2016}, + doi = {arXiv:1605.06336}, + url = {https://arxiv.org/pdf/1605.06336.pdf}, + file = {papers/Hyvarinen_arXiv2016.pdf} +} + +@incollection{Du_2019, + doi = {10.1007/978-1-4471-7452-3_2}, + url = {https://doi.org/10.1007/2F978-1-4471-7452-3_2}, + year = 2019, + publisher = {Springer London}, + pages = {21--63}, + author = {Ke-Lin Du and M. N. S. Swamy}, + title = {Fundamentals of Machine Learning}, + booktitle = {Neural Networks and Statistical Learning}, + file = {papers/2019_Book_NeuralNetworksAndStatisticalLe.pdf} +} + +@article{Oja1982, + title = {A simplified neuron model as a principal component analyzer.}, + author = {Oja, E}, + journal = {J Math Biol}, + volume = {15}, + number = {3}, + year = {1982}, + pages = {267-73}, + pubmed = {7153672}, + doi = {10.1007/BF00275687}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/7153672}, + file = {papers/Oja_JMathBiol1982-7153672.pdf}, + nlmuniqueid = {7502105} +} + +@book{Hyvarinen_2001, + doi = {10.1002/0471221317}, + url = {https://doi.org/10.1002/2F0471221317}, + url2 = {https://onlinelibrary.wiley.com/doi/book/10.1002/0471221317}, + year = {2001}, + month = {may}, + publisher = {John Wiley {\&} Sons, Inc.}, + author = {Aapo Hyvärinen and Juha Karhunen and Erkki Oja}, + title = {Independent Component Analysis}, + file = {papers/Hyvarinen2001_bookfinal_ICA.pdf} +} + +@book{2015_ICA_learning, + doi = {10.1016/C2014-0-02754-2}, + url = {https://doi.org/10.1016/C2014-0-02754-2}, + url2 = {https://www.sciencedirect.com/book/9780128028063/advances-in-independent-component-analysis-and-learning-machines#book-description}, + year = {2015}, + publisher = {Elsevier}, + author = {Bingham, Ella and Kaski, Samuel and Laaksonen, Jorma and Lampinen, Jouko}, + title = {Advances in Independent Component Analysis and Learning Machines}, + file = {papers/2015_Advances-in-Independent-Component-Analysis-and-Learning-Machines.pdf} +} + +@article{Berkes2011, + title = {Spontaneous cortical activity reveals hallmarks of an optimal internal model of the environment.}, + author = {Berkes, Pietro and Orbán, Gergo and Lengyel, Máté and Fiser, József}, + journal = {Science}, + volume = {331}, + number = {6013}, + year = {2011}, + month = {Jan}, + pages = {83-7}, + abstract = {The brain maintains internal models of its environment to interpret sensory inputs and to prepare actions. Although behavioral studies have demonstrated that these internal models are optimally adapted to the statistics of the environment, the neural underpinning of this adaptation is unknown. Using a Bayesian model of sensory cortical processing, we related stimulus-evoked and spontaneous neural activities to inferences and prior expectations in an internal model and predicted that they should match if the model is statistically optimal. To test this prediction, we analyzed visual cortical activity of awake ferrets during development. Similarity between spontaneous and evoked activities increased with age and was specific to responses evoked by natural scenes. This demonstrates the progressive adaptation of internal models to the statistics of natural stimuli at the neural level.}, + pubmed = {21212356}, + pii = {331/6013/83}, + doi = {10.1126/science.1195870}, + pmc = {PMC3065813}, + mid = {UKMS33678}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/21212356}, + file = {papers/Berkes_Science2011-21212356.pdf}, + nlmuniqueid = {0404511} +} + +@article{Chestek2007, + title = {Single-neuron stability during repeated reaching in macaque premotor cortex.}, + author = {Chestek, Cynthia A and Batista, Aaron P and Santhanam, Gopal and Yu, Byron M and Afshar, Afsheen and Cunningham, John P and Gilja, Vikash and Ryu, Stephen I and Churchland, Mark M and Shenoy, Krishna V}, + journal = {J Neurosci}, + volume = {27}, + number = {40}, + year = {2007}, + month = {Oct}, + pages = {10742-50}, + abstract = {Some movements that animals and humans make are highly stereotyped, repeated with little variation. The patterns of neural activity associated with repeats of a movement may be highly similar, or the same movement may arise from different patterns of neural activity, if the brain exploits redundancies in the neural projections to muscles. We examined the stability of the relationship between neural activity and behavior. We asked whether the variability in neural activity that we observed during repeated reaching was consistent with a noisy but stable relationship, or with a changing relationship, between neural activity and behavior. Monkeys performed highly similar reaches under tight behavioral control, while many neurons in the dorsal aspect of premotor cortex and the primary motor cortex were simultaneously monitored for several hours. Neural activity was predominantly stable over time in all measured properties: firing rate, directional tuning, and contribution to a decoding model that predicted kinematics from neural activity. The small changes in neural activity that we did observe could be accounted for primarily by subtle changes in behavior. We conclude that the relationship between neural activity and practiced behavior is reasonably stable, at least on timescales of minutes up to 48 h. This finding has significant implications for the design of neural prosthetic systems because it suggests that device recalibration need not be overly frequent, It also has implications for studies of neural plasticity because a stable baseline permits identification of nonstationary shifts.}, + pubmed = {17913908}, + pii = {27/40/10742}, + doi = {10.1523/JNEUROSCI.0959-07.2007}, + pmc = {PMC6672821}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/17913908}, + file = {papers/Chestek_JNeurosci2007-17913908.pdf}, + nlmuniqueid = {8102140} +} + +@article{Gămănuţ2018, + title = {The Mouse Cortical Connectome, Characterized by an Ultra-Dense Cortical Graph, Maintains Specificity by Distinct Connectivity Profiles.}, + author = {Gămănuţ, Răzvan and Kennedy, Henry and Toroczkai, Zoltán and Ercsey-Ravasz, Mária and Van Essen, David C and Knoblauch, Kenneth and Burkhalter, Andreas}, + journal = {Neuron}, + volume = {97}, + number = {3}, + year = {2018}, + month = {02}, + pages = {698-715.e10}, + abstract = {The inter-areal wiring pattern of the mouse cerebral cortex was analyzed in relation to a refined parcellation of cortical areas. Twenty-seven retrograde tracer injections were made in 19 areas of a 47-area parcellation of the mouse neocortex. Flat mounts of the cortex and multiple histological markers enabled detailed counts of labeled neurons in individual areas. The observed log-normal distribution of connection weights to each cortical area spans 5 orders of magnitude and reveals a distinct connectivity profile for each area, analogous to that observed in macaques. The cortical network has a density of 97%, considerably higher than the 66% density reported in macaques. A weighted graph analysis reveals a similar global efficiency but weaker spatial clustering compared with that reported in macaques. The consistency, precision of the connectivity profile, density, and weighted graph analysis of the present data differ significantly from those obtained in earlier studies in the mouse.}, + keywords = {anatomy; connectivity; log-normal; neocortex; retrograde; rodent; tract-tracing; Animals; Connectome; Female; Macaca; Male; Models, Neurological; Neocortex; Neural Pathways; Neuroanatomical Tract-Tracing Techniques; Species Specificity; }, + pubmed = {29420935}, + pii = {S0896-6273(17)31185-6}, + doi = {10.1016/j.neuron.2017.12.037}, + pmc = {PMC5958229}, + mid = {NIHMS931062}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/29420935}, + file = {papers/Gămănuţ_Neuron2018-29420935.pdf}, + nlmuniqueid = {8809320} +} + +@article{Gomez-Marin2019, + title = {The Life of Behavior.}, + author = {Gomez-Marin, Alex and Ghazanfar, Asif A}, + journal = {Neuron}, + volume = {104}, + number = {1}, + year = {2019}, + month = {10}, + pages = {25-36}, + abstract = {Neuroscience needs behavior. However, it is daunting to render the behavior of organisms intelligible without suppressing most, if not all, references to life. When animals are treated as passive stimulus-response, disembodied and identical machines, the life of behavior perishes. Here, we distill three biological principles (materiality, agency, and historicity), spell out their consequences for the study of animal behavior, and illustrate them with various examples from the literature. We propose to put behavior back into context, with the brain in a species-typical body and with the animal's body situated in the world; stamp Newtonian time with nested ontogenetic and phylogenetic processes that give rise to individuals with their own histories; and supplement linear cause-and-effect chains and information processing with circular loops of purpose and meaning. We believe that conceiving behavior in these ways is imperative for neuroscience.}, + pubmed = {31600513}, + pii = {S0896-6273(19)30790-1}, + doi = {10.1016/j.neuron.2019.09.017}, + pmc = {PMC6873815}, + mid = {NIHMS1543024}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/31600513}, + file = {papers/Gomez-Marin_Neuron2019-31600513.pdf}, + nlmuniqueid = {8809320} +} + +@article{Mazade2019, + title = {Synergy in Cortical Networks.}, + author = {Mazade, Reece and Alonso, Jose Manuel}, + journal = {Neuron}, + volume = {104}, + number = {2}, + year = {2019}, + month = {10}, + pages = {184-185}, + abstract = {A dot in this text can simultaneously stimulate thousands of neurons in primary visual cortex, a response that may seem unnecessarily redundant. Contrary to such a view, in this issue of Neuron, Nigam et al. (2019) demonstrate that these co-activated neurons generate abundant synergistic interactions that help to decode the stimulus.}, + pubmed = {31647891}, + pii = {S0896-6273(19)30844-X}, + doi = {10.1016/j.neuron.2019.09.041}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/31647891}, + file = {papers/Mazade_Neuron2019-31647891.pdf}, + nlmuniqueid = {8809320} +} + +@article{Fujisawa2011, + title = {A 4 Hz oscillation adaptively synchronizes prefrontal, VTA, and hippocampal activities.}, + author = {Fujisawa, Shigeyoshi and Buzsáki, György}, + journal = {Neuron}, + volume = {72}, + number = {1}, + year = {2011}, + month = {Oct}, + pages = {153-65}, + abstract = {Network oscillations support transient communication across brain structures. We show here, in rats, that task-related neuronal activity in the medial prefrontal cortex (PFC), the hippocampus, and the ventral tegmental area (VTA), regions critical for working memory, is coordinated by a 4 Hz oscillation. A prominent increase of power and coherence of the 4 Hz oscillation in the PFC and the VTA and its phase modulation of gamma power in both structures was present in the working memory part of the task. Subsets of both PFC and hippocampal neurons predicted the turn choices of the rat. The goal-predicting PFC pyramidal neurons were more strongly phase locked to both 4 Hz and hippocampal theta oscillations than nonpredicting cells. The 4 Hz and theta oscillations were phase coupled and jointly modulated both gamma waves and neuronal spikes in the PFC, the VTA, and the hippocampus. Thus, multiplexed timing mechanisms in the PFC-VTA-hippocampus axis may support processing of information, including working memory.}, + pubmed = {21982376}, + pii = {S0896-6273(11)00739-2}, + doi = {10.1016/j.neuron.2011.08.018}, + pmc = {PMC3235795}, + mid = {NIHMS321938}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/21982376}, + file = {papers/Fujisawa_Neuron2011-21982376.pdf}, + nlmuniqueid = {8809320} +} + +@article{Sejnowski2020, + title = {The unreasonable effectiveness of deep learning in artificial intelligence.}, + author = {Sejnowski, Terrence J}, + journal = {Proc Natl Acad Sci U S A}, + volume = {117}, + number = {48}, + year = {2020}, + month = {12}, + pages = {30033-30038}, + abstract = {Deep learning networks have been trained to recognize speech, caption photographs, and translate text between languages at high levels of performance. Although applications of deep learning networks to real-world problems have become ubiquitous, our understanding of why they are so effective is lacking. These empirical results should not be possible according to sample complexity in statistics and nonconvex optimization theory. However, paradoxes in the training and effectiveness of deep learning networks are being investigated and insights are being found in the geometry of high-dimensional spaces. A mathematical theory of deep learning would illuminate how they function, allow us to assess the strengths and weaknesses of different network architectures, and lead to major improvements. Deep learning has provided natural ways for humans to communicate with digital devices and is foundational for building artificial general intelligence. Deep learning was inspired by the architecture of the cerebral cortex and insights into autonomy and general intelligence may be found in other brain regions that are essential for planning and survival, but major breakthroughs will be needed to achieve these goals.}, + keywords = {artificial intelligence; deep learning; neural networks; }, + pubmed = {31992643}, + pii = {1907373117}, + doi = {10.1073/pnas.1907373117}, + pmc = {PMC7720171}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/31992643}, + file = {papers/Sejnowski_ProcNatlAcadSciUSA2020-31992643.pdf}, + nlmuniqueid = {7505876} +} + +@article{Peters_2019, + doi = {10.1038/s41567-019-0732-0}, + url = {https://doi.org/10.1038%2Fs41567-019-0732-0}, + year = 2019, + month = {dec}, + publisher = {Springer Science and Business Media {LLC}}, + volume = {15}, + number = {12}, + pages = {1216--1221}, + author = {Ole Peters}, + title = {The ergodicity problem in economics}, + journal = {Nature Physics}, + file = {papers/Peters_NaturePhysics2019.pdf} +} + +@article{Barson2020, + title = {Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits.}, + author = {Barson, Daniel and Hamodi, Ali S and Shen, Xilin and Lur, Gyorgy and Constable, R Todd and Cardin, Jessica A and Crair, Michael C and Higley, Michael J}, + journal = {Nat Methods}, + volume = {17}, + number = {1}, + year = {2020}, + month = {01}, + pages = {107-113}, + abstract = {Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium imaging of a local microcircuit and mesoscopic widefield calcium imaging of the entire cortical mantle in awake mice. Our multi-scale approach involves a microscope with an orthogonal axis design where the mesoscopic objective is oriented above the brain and the two-photon objective is oriented horizontally, with imaging performed through a microprism. We also introduce a viral transduction method for robust and widespread gene delivery in the mouse brain. These approaches allow us to identify the behavioral state-dependent functional connectivity of pyramidal neurons and vasoactive intestinal peptide-expressing interneurons with long-range cortical networks. Our imaging system provides a powerful strategy for investigating cortical architecture across a wide range of spatial scales.}, + pubmed = {31686040}, + doi = {10.1038/s41592-019-0625-2}, + pii = {10.1038/s41592-019-0625-2}, + pmc = {PMC6946863}, + mid = {NIHMS1540817}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/31686040}, + file = {papers/Barson_NatMethods2020-31686040.pdf}, + nlmuniqueid = {101215604} +} + +@article{Zhu2018, + title = {Decoding cortical brain states from widefield calcium imaging data using visibility graph.}, + author = {Zhu, Li and Lee, Christian R and Margolis, David J and Najafizadeh, Laleh}, + journal = {Biomed Opt Express}, + volume = {9}, + number = {7}, + year = {2018}, + month = {Jul}, + pages = {3017-3036}, + abstract = {Widefield optical imaging of neuronal populations over large portions of the cerebral cortex in awake behaving animals provides a unique opportunity for investigating the relationship between brain function and behavior. In this paper, we demonstrate that the temporal characteristics of calcium dynamics obtained through widefield imaging can be utilized to infer the corresponding behavior. Cortical activity in transgenic calcium reporter mice (n=6) expressing GCaMP6f in neocortical pyramidal neurons is recorded during active whisking (AW) and no whisking (NW). To extract features related to the temporal characteristics of calcium recordings, a method based on visibility graph (VG) is introduced. An extensive study considering different choices of features and classifiers is conducted to find the best model capable of predicting AW and NW from calcium recordings. Our experimental results show that temporal characteristics of calcium recordings identified by the proposed method carry discriminatory information that are powerful enough for decoding behavior.}, + keywords = {(170.2655) Functional monitoring and imaging; (170.3880) Medical and biological imaging; }, + pubmed = {29984080}, + doi = {10.1364/BOE.9.003017}, + pii = {320299}, + pmc = {PMC6033549}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/29984080}, + file = {papers/Zhu_BiomedOptExpress2018-29984080.pdf}, + nlmuniqueid = {101540630} +} + +@article{Silasi2016, + title = {Intact skull chronic windows for mesoscopic wide-field imaging in awake mice.}, + author = {Silasi, Gergely and Xiao, Dongsheng and Vanni, Matthieu P and Chen, Andrew C N and Murphy, Timothy H}, + journal = {J Neurosci Methods}, + volume = {267}, + year = {2016}, + month = {07}, + pages = {141-9}, + abstract = {Craniotomy-based window implants are commonly used for microscopic imaging, in head-fixed rodents, however their field of view is typically small and incompatible with mesoscopic functional mapping of cortex.}, + keywords = {GCaMP; Head-fixed; Optogenetics; Animals; Cerebral Cortex; Craniotomy; Dental Cements; Equipment Design; Glass; Grooming; Longitudinal Studies; Mice, Transgenic; Motor Activity; Neuroimaging; Optical Imaging; Optogenetics; Prostheses and Implants; Skull; Time Factors; Wakefulness; }, + pubmed = {27102043}, + pmc = {PMC5075450}, + pii = {S0165-0270(16)30064-4}, + doi = {10.1016/j.jneumeth.2016.04.012}, + mid = {CAMS6038}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/27102043}, + file = {papers/Silasi_JNeurosciMethods2016-27102043.pdf}, + nlmuniqueid = {7905558} +} + +@article{Cramer2019, + title = {In vivo widefield calcium imaging of the mouse cortex for analysis of network connectivity in health and brain disease.}, + author = {Cramer, Julia V and Gesierich, Benno and Roth, Stefan and Dichgans, Martin and Düring, Marco and Liesz, Arthur}, + journal = {Neuroimage}, + volume = {199}, + year = {2019}, + month = {10}, + pages = {570-584}, + abstract = {The organization of brain areas in functionally connected networks, their dynamic changes, and perturbations in disease states are subject of extensive investigations. Research on functional networks in humans predominantly uses functional magnetic resonance imaging (fMRI). However, adopting fMRI and other functional imaging methods to mice, the most widely used model to study brain physiology and disease, poses major technical challenges and faces important limitations. Hence, there is great demand for alternative imaging modalities for network characterization. Here, we present a refined protocol for in vivo widefield calcium imaging of both cerebral hemispheres in mice expressing a calcium sensor in excitatory neurons. We implemented a stringent protocol for minimizing anesthesia and excluding movement artifacts which both imposed problems in previous approaches. We further adopted a method for unbiased identification of functional cortical areas using independent component analysis (ICA) on resting-state imaging data. Biological relevance of identified components was confirmed using stimulus-dependent cortical activation. To explore this novel approach in a model of focal brain injury, we induced photothrombotic lesions of the motor cortex, determined changes in inter- and intrahemispheric connectivity at multiple time points up to 56 days post-stroke and correlated them with behavioral deficits. We observed a severe loss in interhemispheric connectivity after stroke, which was partially restored in the chronic phase and associated with corresponding behavioral motor deficits. Taken together, we present an improved widefield calcium imaging tool accounting for anesthesia and movement artifacts, adopting an advanced analysis pipeline based on human fMRI algorithms and with superior sensitivity to recovery mechanisms in mouse models compared to behavioral tests. This tool will enable new studies on interhemispheric connectivity in murine models with comparability to human imaging studies for a wide spectrum of neuroscience applications in health and disease.}, + keywords = {ICA; In vivo imaging; Mouse models; Neuronal network connectivity; Recovery; Stroke; Animals; Calcium; Cerebral Cortex; Connectome; Disease Models, Animal; Female; Male; Mice; Mice, Inbred C57BL; Motor Cortex; Nerve Net; Neuroimaging; Optical Imaging; Prosencephalon; Stroke; }, + pubmed = {31181333}, + pii = {S1053-8119(19)30499-9}, + doi = {10.1016/j.neuroimage.2019.06.014}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/31181333}, + file = {papers/Cramer_Neuroimage2019-31181333.pdf}, + nlmuniqueid = {9215515} +} + +@article{Shore2020, + title = {Reduced GABAergic Neuron Excitability, Altered Synaptic Connectivity, and Seizures in a KCNT1 Gain-of-Function Mouse Model of Childhood Epilepsy.}, + author = {Shore, Amy N and Colombo, Sophie and Tobin, William F and Petri, Sabrina and Cullen, Erin R and Dominguez, Soledad and Bostick, Christopher D and Beaumont, Michael A and Williams, Damian and Khodagholy, Dion and Yang, Mu and Lutz, Cathleen M and Peng, Yueqing and Gelinas, Jennifer N and Goldstein, David B and Boland, Michael J and Frankel, Wayne N and Weston, Matthew C}, + journal = {Cell Rep}, + volume = {33}, + number = {4}, + year = {2020}, + month = {10}, + pages = {108303}, + abstract = {Gain-of-function (GOF) variants in K+ channels cause severe childhood epilepsies, but there are no mechanisms to explain how increased K+ currents lead to network hyperexcitability. Here, we introduce a human Na+-activated K+ (KNa) channel variant (KCNT1-Y796H) into mice and, using a multiplatform approach, find motor cortex hyperexcitability and early-onset seizures, phenotypes strikingly similar to those of human patients. Although the variant increases KNa currents in cortical excitatory and inhibitory neurons, there is an increase in the KNa current across subthreshold voltages only in inhibitory neurons, particularly in those with non-fast-spiking properties, resulting in inhibitory-neuron-specific impairments in excitability and action potential (AP) generation. We further observe evidence of synaptic rewiring, including increases in homotypic synaptic connectivity, accompanied by network hyperexcitability and hypersynchronicity. These findings support inhibitory-neuron-specific mechanisms in mediating the epileptogenic effects of KCNT1 channel GOF, offering cell-type-specific currents and effects as promising targets for therapeutic intervention.}, + keywords = {ADNFLE; K(Na) current; KCNT1; MEA; Slack; calcium imaging; electrocorticography; electrophysiology; epilepsy; synaptic transmission; }, + pubmed = {33113364}, + pii = {S2211-1247(20)31292-4}, + doi = {10.1016/j.celrep.2020.108303}, + pmc = {PMC7712469}, + mid = {NIHMS1642113}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/33113364}, + file = {papers/Shore_CellRep2020-33113364.pdf}, + nlmuniqueid = {101573691} +} + +@article{Murphy2020, + title = {Automated task training and longitudinal monitoring of mouse mesoscale cortical circuits using home cages.}, + author = {Murphy, Timothy H and Michelson, Nicholas J and Boyd, Jamie D and Fong, Tony and Bolanos, Luis A and Bierbrauer, David and Siu, Teri and Balbi, Matilde and Bolanos, Federico and Vanni, Matthieu and LeDue, Jeff M}, + journal = {Elife}, + volume = {9}, + year = {2020}, + month = {05}, + pages = {}, + abstract = {We report improved automated open-source methodology for head-fixed mesoscale cortical imaging and/or behavioral training of home cage mice using Raspberry Pi-based hardware. Staged partial and probabilistic restraint allows mice to adjust to self-initiated headfixation over 3 weeks' time with ~50% participation rate. We support a cue-based behavioral licking task monitored by a capacitive touch-sensor water spout. While automatically head-fixed, we acquire spontaneous, movement-triggered, or licking task-evoked GCaMP6 cortical signals. An analysis pipeline marked both behavioral events, as well as analyzed brain fluorescence signals as they relate to spontaneous and/or task-evoked behavioral activity. Mice were trained to suppress licking and wait for cues that marked the delivery of water. Correct rewarded go-trials were associated with widespread activation of midline and lateral barrel cortex areas following a vibration cue and delayed frontal and lateral motor cortex activation. Cortical GCaMP signals predicted trial success and correlated strongly with trial-outcome dependent body movements.}, + keywords = {automation; cortex; homecage; imaging; mesoscale; mouse; neuroscience; Animals; Behavior, Animal; Brain Mapping; Calcium-Binding Proteins; Cues; Drinking; Equipment Design; Female; Head Movements; Luminescent Proteins; Male; Mice, Inbred C57BL; Mice, Transgenic; Motor Cortex; Optical Imaging; Restraint, Physical; Reward; Time Factors; }, + pubmed = {32412409}, + doi = {10.7554/eLife.55964}, + pii = {55964}, + pmc = {PMC7332290}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/32412409}, + file = {papers/Murphy_Elife2020-32412409.pdf}, + nlmuniqueid = {101579614} +} + +@article{Lake2020, + title = {Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI.}, + author = {Lake, Evelyn M R and Ge, Xinxin and Shen, Xilin and Herman, Peter and Hyder, Fahmeed and Cardin, Jessica A and Higley, Michael J and Scheinost, Dustin and Papademetris, Xenophon and Crair, Michael C and Constable, R Todd}, + journal = {Nat Methods}, + volume = {17}, + number = {12}, + year = {2020}, + month = {12}, + pages = {1262-1271}, + abstract = {Achieving a comprehensive understanding of brain function requires multiple imaging modalities with complementary strengths. We present an approach for concurrent widefield optical and functional magnetic resonance imaging. By merging these modalities, we can simultaneously acquire whole-brain blood-oxygen-level-dependent (BOLD) and whole-cortex calcium-sensitive fluorescent measures of brain activity. In a transgenic murine model, we show that calcium predicts the BOLD signal, using a model that optimizes a gamma-variant transfer function. We find consistent predictions across the cortex, which are best at low frequency (0.009-0.08 Hz). Furthermore, we show that the relationship between modality connectivity strengths varies by region. Our approach links cell-type-specific optical measurements of activity to the most widely used method for assessing human brain function.}, + pubmed = {33139894}, + doi = {10.1038/s41592-020-00984-6}, + pii = {10.1038/s41592-020-00984-6}, + pmc = {PMC7704940}, + mid = {NIHMS1631388}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/33139894}, + file = {papers/Lake_NatMethods2020-33139894.pdf}, + nlmuniqueid = {101215604} +} + +@article{Valley2020, + title = {Separation of hemodynamic signals from GCaMP fluorescence measured with wide-field imaging.}, + author = {Valley, M T and Moore, M G and Zhuang, J and Mesa, N and Castelli, D and Sullivan, D and Reimers, M and Waters, J}, + journal = {J Neurophysiol}, + volume = {123}, + number = {1}, + year = {2020}, + month = {01}, + pages = {356-366}, + abstract = {Wide-field calcium imaging is often used to measure brain dynamics in behaving mice. With a large field of view and a high sampling rate, wide-field imaging can monitor activity from several distant cortical areas simultaneously, revealing cortical interactions. Interpretation of wide-field images is complicated, however, by the absorption of light by hemoglobin, which can substantially affect the measured fluorescence. One approach to separating hemodynamics and calcium signals is to use multiwavelength backscatter recordings to measure light absorption by hemoglobin. Following this approach, we develop a spatially detailed regression-based method to estimate hemodynamics. This Spatial Model is based on a linear form of the Beer-Lambert relationship but is fit at every pixel in the image and does not rely on the estimation of physical parameters. In awake mice of three transgenic lines, the Spatial Model offers improved separation of hemodynamics and changes in GCaMP fluorescence. The improvement is pronounced near blood vessels and, in contrast with the Beer-Lambert equations, can remove vascular artifacts along the sagittal midline and in general permits more accurate fluorescence-based determination of neuronal activity across the cortex.NEW & NOTEWORTHY This paper addresses a well-known and strong source of contamination in wide-field calcium-imaging data: hemodynamics. To guide researchers toward the best method to separate calcium signals from hemodynamics, we compare the performance of several methods in three commonly used mouse lines and present a novel regression model that outperforms the other techniques we consider.}, + keywords = {animal behavior; calcium imaging; hemodynamics; optical methods; systems neuroscience; }, + pubmed = {31747332}, + doi = {10.1152/jn.00304.2019}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/31747332}, + file = {papers/Valley_JNeurophysiol2020-31747332.pdf}, + nlmuniqueid = {0375404} +} + +@article{Peters_2019, + doi = {10.1038/s41567-019-0732-0}, + url = {https://doi.org/10.1038%2Fs41567-019-0732-0}, + year = 2019, + month = {dec}, + publisher = {Springer Science and Business Media {LLC}}, + volume = {15}, + number = {12}, + pages = {1216--1221}, + author = {Ole Peters}, + title = {The ergodicity problem in economics}, + journal = {Nature Physics} +} + +@article{Aruljothi2020, + title = {Functional Localization of an Attenuating Filter within Cortex for a Selective Detection Task in Mice.}, + author = {Aruljothi, Krithiga and Marrero, Krista and Zhang, Zhaoran and Zareian, Behzad and Zagha, Edward}, + journal = {J Neurosci}, + volume = {40}, + number = {28}, + year = {2020}, + month = {07}, + pages = {5443-5454}, + abstract = {An essential feature of goal-directed behavior is the ability to selectively respond to the diverse stimuli in one's environment. However, the neural mechanisms that enable us to respond to target stimuli while ignoring distractor stimuli are poorly understood. To study this sensory selection process, we trained male and female mice in a selective detection task in which mice learn to respond to rapid stimuli in the target whisker field and ignore identical stimuli in the opposite, distractor whisker field. In expert mice, we used widefield Ca2+ imaging to analyze target-related and distractor-related neural responses throughout dorsal cortex. For target stimuli, we observed strong signal activation in primary somatosensory cortex (S1) and frontal cortices, including both the whisker region of primary motor cortex (wMC) and anterior lateral motor cortex (ALM). For distractor stimuli, we observed strong signal activation in S1, with minimal propagation to frontal cortex. Our data support only modest subcortical filtering, with robust, step-like attenuation in distractor processing between mono-synaptically coupled regions of S1 and wMC. This study establishes a highly robust model system for studying the neural mechanisms of sensory selection and places important constraints on its implementation.SIGNIFICANCE STATEMENT Responding to task-relevant stimuli while ignoring task-irrelevant stimuli is critical for goal-directed behavior. However, the neural mechanisms involved in this selection process are poorly understood. We trained mice in a detection task with both target and distractor stimuli. During expert performance, we measured neural activity throughout cortex using widefield imaging. We observed responses to target stimuli in multiple sensory and motor cortical regions. In contrast, responses to distractor stimuli were abruptly suppressed beyond sensory cortex. Our findings localize the sites of attenuation when successfully ignoring a distractor stimulus and provide essential foundations for further revealing the neural mechanism of sensory selection and distractor suppression.}, + keywords = {attenuating filter; neocortex; sensorimotor; sensory selection; somatosensory; widefield imaging; Animals; Attention; Female; Male; Mice; Motor Cortex; Physical Stimulation; Reaction Time; Somatosensory Cortex; Touch Perception; Vibrissae; }, + pubmed = {32487695}, + pii = {JNEUROSCI.2993-19.2020}, + doi = {10.1523/JNEUROSCI.2993-19.2020}, + pmc = {PMC7343319}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/32487695}, + file = {papers/Aruljothi_JNeurosci2020-32487695.pdf}, + nlmuniqueid = {8102140} +} + +@article{Nobre2020, + title = {Under the Mind's Hood: What We Have Learned by Watching the Brain at Work.}, + author = {Nobre, Anna Christina and van Ede, Freek}, + journal = {J Neurosci}, + volume = {40}, + number = {1}, + year = {2020}, + month = {01}, + pages = {89-100}, + abstract = {Imagine you were asked to investigate the workings of an engine, but to do so without ever opening the hood. Now imagine the engine fueled the human mind. This is the challenge faced by cognitive neuroscientists worldwide aiming to understand the neural bases of our psychological functions. Luckily, human ingenuity comes to the rescue. Around the same time as the Society for Neuroscience was being established in the 1960s, the first tools for measuring the human brain at work were becoming available. Noninvasive human brain imaging and neurophysiology have continued developing at a relentless pace ever since. In this 50 year anniversary, we reflect on how these methods have been changing our understanding of how brain supports mind.}, + keywords = {Electroencephalograhy (EEG); Functional Magnetic Resonance Imaging (fMRI); Historical overview; Human brain imaging; Human neurophysiology; Selective attention; Attention; Brain Mapping; Cognition; Evoked Potentials; Forecasting; History, 19th Century; History, 20th Century; History, 21st Century; Humans; Machine Learning; Mental Processes; Neuroimaging; Neurophysiology; Neuropsychology; Psychophysiology; }, + pubmed = {31630115}, + pii = {JNEUROSCI.0742-19.2019}, + doi = {10.1523/JNEUROSCI.0742-19.2019}, + pmc = {PMC6939481}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/31630115}, + file = {papers/Nobre_JNeurosci2020-31630115.pdf}, + nlmuniqueid = {8102140} +} + +@article{Vu2018, + title = {A Shared Vision for Machine Learning in Neuroscience.}, + author = {Vu, Mai-Anh T and Adalı, Tülay and Ba, Demba and Buzsáki, György and Carlson, David and Heller, Katherine and Liston, Conor and Rudin, Cynthia and Sohal, Vikaas S and Widge, Alik S and Mayberg, Helen S and Sapiro, Guillermo and Dzirasa, Kafui}, + journal = {J Neurosci}, + volume = {38}, + number = {7}, + year = {2018}, + month = {02}, + pages = {1601-1607}, + abstract = {With ever-increasing advancements in technology, neuroscientists are able to collect data in greater volumes and with finer resolution. The bottleneck in understanding how the brain works is consequently shifting away from the amount and type of data we can collect and toward what we actually do with the data. There has been a growing interest in leveraging this vast volume of data across levels of analysis, measurement techniques, and experimental paradigms to gain more insight into brain function. Such efforts are visible at an international scale, with the emergence of big data neuroscience initiatives, such as the BRAIN initiative (Bargmann et al., 2014), the Human Brain Project, the Human Connectome Project, and the National Institute of Mental Health's Research Domain Criteria initiative. With these large-scale projects, much thought has been given to data-sharing across groups (Poldrack and Gorgolewski, 2014; Sejnowski et al., 2014); however, even with such data-sharing initiatives, funding mechanisms, and infrastructure, there still exists the challenge of how to cohesively integrate all the data. At multiple stages and levels of neuroscience investigation, machine learning holds great promise as an addition to the arsenal of analysis tools for discovering how the brain works.}, + keywords = {explainable artificial intelligence; machine learning; reinforcement learning; Animals; Big Data; Brain; Connectome; Humans; Information Dissemination; Machine Learning; Neurosciences; Reproducibility of Results; }, + pubmed = {29374138}, + pii = {JNEUROSCI.0508-17.2018}, + doi = {10.1523/JNEUROSCI.0508-17.2018}, + pmc = {PMC5815449}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/29374138}, + file = {papers/Vu_JNeurosci2018-29374138.pdf}, + nlmuniqueid = {8102140} +} + +@article{Huk2018, + title = {Beyond Trial-Based Paradigms: Continuous Behavior, Ongoing Neural Activity, and Natural Stimuli.}, + author = {Huk, Alexander and Bonnen, Kathryn and He, Biyu J}, + journal = {J Neurosci}, + volume = {38}, + number = {35}, + year = {2018}, + month = {08}, + pages = {7551-7558}, + abstract = {The vast majority of experiments examining perception and behavior are conducted using experimental paradigms that adhere to a rigid trial structure: each trial consists of a brief and discrete series of events and is regarded as independent from all other trials. The assumptions underlying this structure ignore the reality that natural behavior is rarely discrete, brain activity follows multiple time courses that do not necessarily conform to the trial structure, and the natural environment has statistical structure and dynamics that exhibit long-range temporal correlation. Modern advances in statistical modeling and analysis offer tools that make it feasible for experiments to move beyond rigid independent and identically distributed trial structures. Here we review literature that serves as evidence for the feasibility and advantages of moving beyond trial-based paradigms to understand the neural basis of perception and cognition. Furthermore, we propose a synthesis of these efforts, integrating the characterization of natural stimulus properties with measurements of continuous neural activity and behavioral outputs within the framework of sensory-cognitive-motor loops. Such a framework provides a basis for the study of natural statistics, naturalistic tasks, and/or slow fluctuations in brain activity, which should provide starting points for important generalizations of analytical tools in neuroscience and subsequent progress in understanding the neural basis of perception and cognition.}, + pubmed = {30037835}, + pii = {JNEUROSCI.1920-17.2018}, + doi = {10.1523/JNEUROSCI.1920-17.2018}, + pmc = {PMC6113904}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/30037835}, + file = {papers/Huk_JNeurosci2018-30037835.pdf}, + nlmuniqueid = {8102140} +} + +@article{Lecoq2019, + title = {Wide. Fast. Deep: Recent Advances in Multiphoton Microscopy of In Vivo Neuronal Activity.}, + author = {Lecoq, Jérôme and Orlova, Natalia and Grewe, Benjamin F}, + journal = {J Neurosci}, + volume = {39}, + number = {46}, + year = {2019}, + month = {11}, + pages = {9042-9052}, + abstract = {Multiphoton microscopy (MPM) has emerged as one of the most powerful and widespread technologies to monitor the activity of neuronal networks in awake, behaving animals over long periods of time. MPM development spanned across decades and crucially depended on the concurrent improvement of calcium indicators that report neuronal activity as well as surgical protocols, head fixation approaches, and innovations in optics and microscopy technology. Here we review the last decade of MPM development and highlight how in vivo imaging has matured and diversified, making it now possible to concurrently monitor thousands of neurons across connected brain areas or, alternatively, small local networks with sampling rates in the kilohertz range. This review includes different laser scanning approaches, such as multibeam technologies as well as recent developments to image deeper into neuronal tissues using new, long-wavelength laser sources. As future development will critically depend on our ability to resolve and discriminate individual neuronal spikes, we will also describe a simple framework that allows performing quantitative comparisons between the reviewed MPM instruments. Finally, we provide our own opinion on how the most recent MPM developments can be leveraged at scale to enable the next generation of discoveries in brain function.}, + keywords = {imaging; in vivo; multiphoton; two-photon; Animals; Brain; Image Processing, Computer-Assisted; Microscopy, Confocal; Microscopy, Fluorescence, Multiphoton; Neurons; }, + pubmed = {31578235}, + pii = {JNEUROSCI.1527-18.2019}, + doi = {10.1523/JNEUROSCI.1527-18.2019}, + pmc = {PMC6855689}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/31578235}, + file = {papers/Lecoq_JNeurosci2019-31578235.pdf}, + nlmuniqueid = {8102140} +} + +@article{Bassett2017, + title = {Network neuroscience.}, + author = {Bassett, Danielle S and Sporns, Olaf}, + journal = {Nat Neurosci}, + volume = {20}, + number = {3}, + year = {2017}, + month = {Feb}, + pages = {353-364}, + abstract = {Despite substantial recent progress, our understanding of the principles and mechanisms underlying complex brain function and cognition remains incomplete. Network neuroscience proposes to tackle these enduring challenges. Approaching brain structure and function from an explicitly integrative perspective, network neuroscience pursues new ways to map, record, analyze and model the elements and interactions of neurobiological systems. Two parallel trends drive the approach: the availability of new empirical tools to create comprehensive maps and record dynamic patterns among molecules, neurons, brain areas and social systems; and the theoretical framework and computational tools of modern network science. The convergence of empirical and computational advances opens new frontiers of scientific inquiry, including network dynamics, manipulation and control of brain networks, and integration of network processes across spatiotemporal domains. We review emerging trends in network neuroscience and attempt to chart a path toward a better understanding of the brain as a multiscale networked system.}, + pubmed = {28230844}, + pii = {nn.4502}, + doi = {10.1038/nn.4502}, + pmc = {PMC5485642}, + mid = {NIHMS855763}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/28230844}, + file = {papers/Bassett_NatNeurosci2017-28230844.pdf}, + nlmuniqueid = {9809671} +} + +@article{Gomez-Marin2021, + title = {Promisomics and the Short-Circuiting of Mind.}, + author = {Gomez-Marin, Alex}, + journal = {eNeuro}, + volume = {8}, + number = {2}, + pages = {}, + keywords = {cognition; connectomics; levels of analysis; promissory materialism; }, + pubmed = {33648976}, + pii = {ENEURO.0521-20.2021}, + doi = {10.1523/ENEURO.0521-20.2021}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/33648976}, + file = {papers/Gomez-Marin_eNeuro-33648976.pdf}, + nlmuniqueid = {101647362} +} + +@article{nnMethodsFocus2020, + title = {Focus on neuroscience methods.}, + journal = {Nat Neurosci}, + volume = {23}, + number = {12}, + year = {2020}, + month = {12}, + pages = {1455}, + pubmed = {33230327}, + doi = {10.1038/s41593-020-00750-z}, + pii = {10.1038/s41593-020-00750-z}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/33230327}, + file = {papers/_NatNeurosci2020-33230327.pdf}, + nlmuniqueid = {9809671} +} + +@article{Yuste2020, + title = {A community-based transcriptomics classification and nomenclature of neocortical cell types.}, + author = {Yuste, Rafael and Hawrylycz, Michael and Aalling, Nadia and Aguilar-Valles, Argel and Arendt, Detlev and Armañanzas, Ruben and Ascoli, Giorgio A and Bielza, Concha and Bokharaie, Vahid and Bergmann, Tobias Borgtoft and Bystron, Irina and Capogna, Marco and Chang, YoonJeung and Clemens, Ann and de Kock, Christiaan P J and DeFelipe, Javier and Dos Santos, Sandra Esmeralda and Dunville, Keagan and Feldmeyer, Dirk and Fiáth, Richárd and Fishell, Gordon James and Foggetti, Angelica and Gao, Xuefan and Ghaderi, Parviz and Goriounova, Natalia A and Güntürkün, Onur and Hagihara, Kenta and Hall, Vanessa Jane and Helmstaedter, Moritz and Herculano-Houzel, Suzana and Hilscher, Markus M and Hirase, Hajime and Hjerling-Leffler, Jens and Hodge, Rebecca and Huang, Josh and Huda, Rafiq and Khodosevich, Konstantin and Kiehn, Ole and Koch, Henner and Kuebler, Eric S and Kühnemund, Malte and Larrañaga, Pedro and Lelieveldt, Boudewijn and Louth, Emma Louise and Lui, Jan H and Mansvelder, Huibert D and Marin, Oscar and Martinez-Trujillo, Julio and Chameh, Homeira Moradi and Mohapatra, Alok Nath and Munguba, Hermany and Nedergaard, Maiken and Němec, Pavel and Ofer, Netanel and Pfisterer, Ulrich Gottfried and Pontes, Samuel and Redmond, William and Rossier, Jean and Sanes, Joshua R and Scheuermann, Richard H and Serrano-Saiz, Esther and Staiger, Jochen F and Somogyi, Peter and Tamás, Gábor and Tolias, Andreas Savas and Tosches, Maria Antonietta and García, Miguel Turrero and Wozny, Christian and Wuttke, Thomas V and Liu, Yong and Yuan, Juan and Zeng, Hongkui and Lein, Ed}, + journal = {Nat Neurosci}, + volume = {23}, + number = {12}, + year = {2020}, + month = {12}, + pages = {1456-1468}, + abstract = {To understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glial cell types, partly due to limited data. Single-cell transcriptomics is enabling, for the first time, systematic high-throughput measurements of cortical cells and generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data reveal clusters that often correspond to cell types previously defined by morphological or physiological criteria and that appear conserved across cortical areas and species. To capitalize on these new methods, we propose the adoption of a transcriptome-based taxonomy of cell types for mammalian neocortex. This classification should be hierarchical and use a standardized nomenclature. It should be based on a probabilistic definition of a cell type and incorporate data from different approaches, developmental stages and species. A community-based classification and data aggregation model, such as a knowledge graph, could provide a common foundation for the study of cortical circuits. This community-based classification, nomenclature and data aggregation could serve as an example for cell type atlases in other parts of the body.}, + pubmed = {32839617}, + doi = {10.1038/s41593-020-0685-8}, + pii = {10.1038/s41593-020-0685-8}, + pmc = {PMC7683348}, + mid = {NIHMS1627961}, + url = {https://www.ncbi.nlm.nih.gov/pubmed/32839617}, + file = {papers/Yuste_NatNeurosci2020-32839617.pdf}, + nlmuniqueid = {9809671} +} + diff --git a/README.md b/README.md index f48267e..7fb814c 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,8 @@ omega.bib : A bibtex data file containing scientific source literature curated ### History -Long ago some of this data started as an endnote/proprietary library file. Then it was a sente/proprietary library for a few years. Once in awhile some of the data would explore other possibilities (papers, zotero, citeulike, mendeley, bookends). But nothing quite fit the combination of truly open/non-proprietary and flexible/hackable/future proofable. - -But then finally the data was freed. It turned into a plain text/open/future proof bibtex file. And there the data has lived happily for ten years. It has enjoyed being managed with the excellent open source BibDesk program long developed for os x/macos. Now it is managed by the equally powerful and feature rich jabref program, which is of course also open source but runs on any platform (a java application) including linux. +Long ago some of this data started as a sequence of non-open library files associated with proprietary programs (endnote, sente in the early-mid 2000s). Once in awhile some of the data would explore other possibilities (papers, citeulike, mendeley, bookends, zotero). But nothing quite fit the combination of truly open/non-proprietary and flexible/hackable/future proofable. +Then the data was freed. It turned into a **plain text**/open/future proof file of a bibtex type format. And there the data has lived happily for ten years, being used with python routines or pandoc for conversion, integration to document prepartion formats intended for web or print publishing. It has enjoyed being managed with the excellent open source BibDesk program long developed for mac osx/macos. It has been also managed by the equally powerful and feature rich jabref program, which is also open source but runs on any platform (as a java application) including linux. In recent times the management has been minimzized (simplified meaning increasingly less external dependencies) with fuzzy-search and bash scripts at the command line. +Methods for transforming the file url links from BibDesk (which were macos specific) are detailed in a separate document '2018-11-01-bibdesk-convert.md'. diff --git a/bibd-md.csl b/bibd-md.csl new file mode 100644 index 0000000..1721ff1 --- /dev/null +++ b/bibd-md.csl @@ -0,0 +1,335 @@ + + diff --git a/bibd-plain.csl b/bibd-plain.csl new file mode 100644 index 0000000..a0502a1 --- /dev/null +++ b/bibd-plain.csl @@ -0,0 +1,333 @@ + + diff --git a/bibd.csl b/bibd.csl new file mode 100644 index 0000000..d3c084a --- /dev/null +++ b/bibd.csl @@ -0,0 +1,335 @@ + +