commit 0e8bdf0e1401dbec3d2641b971bce28538b2e17a Author: ackman678 Date: Wed Mar 13 14:22:03 2019 -0700 init wave diff --git a/README.md b/README.md new file mode 100644 index 0000000..7778f31 --- /dev/null +++ b/README.md @@ -0,0 +1,21 @@ +## biblio database test repo + +Here is a link to a dat blob archive: + + + +Here is another version of that link: + +[The dat link](dat://cdbdaf1e57ddb7066be9c2bee940358b9fbcf779f557e329a4c322b2ef3ea912) is essentially a globally unique identifier (guid) url (using a common, public domain cryptographic hash functions to compute the identifier for your bytes of interest. + +If you are using the Beaker browser or Firefox with the decentralized link(s) plugin for dat or ipfs urls you may be able to click and navigate into the above link to see its content. + +To clone this repo do: + + git clone https://git.ackmanlab.com/jackman/bibd-test.git + +Then within the cloned repo clone the dat archive (install dat first, see me for help or datproject.org): + + cd ~/Downloads/bibd-test/ + dat clone dat://cdbdaf1e57ddb7066be9c2bee940358b9fbcf779f557e329a4c322b2ef3ea912 + diff --git a/wave.bib b/wave.bib new file mode 100644 index 0000000..b9d86f2 --- /dev/null +++ b/wave.bib @@ -0,0 +1,137 @@ +% Encoding: UTF-8 +@article{Belanger:2011a, + Abstract = {The energy requirements of the brain are very high, and tight regulatory mechanisms operate to ensure adequate spatial and temporal delivery of energy substrates in register with neuronal activity. Astrocytes-a type of glial cell-have emerged as active players in brain energy delivery, production, utilization, and storage. Our understanding of neuroenergetics is rapidly evolving from a "neurocentric" view to a more integrated picture involving an intense cooperativity between astrocytes and neurons. This review focuses on the cellular aspects of brain energy metabolism, with a particular emphasis on the metabolic interactions between neurons and astrocytes.}, + Author = {B{\'e}langer, Mireille and Allaman, Igor and Magistretti, Pierre J}, + Date-Added = {2018-09-27 18:53:44 +0000}, + Date-Modified = {2018-09-27 18:53:44 +0000}, + Doi = {10.1016/j.cmet.2011.08.016}, + Journal = {Cell Metab}, + Journal-Full = {Cell metabolism}, + Mesh = {Astrocytes; Brain; Energy Metabolism; Glycogen; Lactic Acid; Models, Biological; Neurons; Oxidative Stress; Regional Blood Flow}, + Month = {Dec}, + Number = {6}, + Pages = {724-38}, + Pmid = {22152301}, + Pst = {ppublish}, + Title = {Brain energy metabolism: focus on astrocyte-neuron metabolic cooperation}, + Volume = {14}, + Year = {2011}, + File = {papers/BeĢlanger_CellMetab2011a.pdf}} + +@article{Joshi:2008, + Abstract = {While progenitor-restricted factors broadly specify area identities in developing neocortex, the downstream regulatory elements involved in acquisition of those identities in postmitotic neurons are largely unknown. Here, we identify Bhlhb5, a transcription factor expressed in layers II-V, as a postmitotic regulator of area identity. Bhlhb5 is initially expressed in a high caudomedial to low rostrolateral gradient that transforms into a sharp border between sensory and rostral motor cortices. Bhlhb5 null mice exhibit aberrant expression of area-specific genes and structural organization in the somatosensory and caudal motor cortices. In somatosensory cortex, Bhlhb5 null mice display postsynaptic disorganization of vibrissal barrels. In caudal motor cortex, Bhlhb5 null mice exhibit anomalous differentiation of corticospinal motor neurons, accompanied by failure of corticospinal tract formation. Together, these results demonstrate Bhlhb5's function as an area-specific transcription factor that regulates the postmitotic acquisition of area identities and elucidate the genetic hierarchy between progenitors and postmitotic neurons driving neocortical arealization.}, + Author = {Joshi, Pushkar S and Molyneaux, Bradley J and Feng, Liang and Xie, Xiaoling and Macklis, Jeffrey D and Gan, Lin}, + Date-Added = {2018-09-18 20:50:58 +0000}, + Date-Modified = {2018-09-18 20:50:58 +0000}, + Doi = {10.1016/j.neuron.2008.08.006}, + Journal = {Neuron}, + Journal-Full = {Neuron}, + Mesh = {Animals; Basic Helix-Loop-Helix Transcription Factors; Body Patterning; Cell Differentiation; Cell Movement; Efferent Pathways; Mice; Mice, Knockout; Mice, Transgenic; Mitosis; Motor Cortex; Neocortex; Neurons; Pyramidal Tracts; Somatosensory Cortex; Stem Cells; Telencephalon; Transcriptional Activation}, + Month = {Oct}, + Number = {2}, + Pages = {258-72}, + Pmc = {PMC2643370}, + Pmid = {18957218}, + Pst = {ppublish}, + Title = {Bhlhb5 regulates the postmitotic acquisition of area identities in layers II-V of the developing neocortex}, + Volume = {60}, + Year = {2008}, + File = {papers/Joshi_Neuron2008.pdf}} + +@article{Strange:2014, + Abstract = {The precise functional role of the hippocampus remains a topic of much debate. The dominant view is that the dorsal (or posterior) hippocampus is implicated in memory and spatial navigation and the ventral (or anterior) hippocampus mediates anxiety-related behaviours. However, this 'dichotomy view' may need revision. Gene expression studies demonstrate multiple functional domains along the hippocampal long axis, which often exhibit sharply demarcated borders. By contrast, anatomical studies and electrophysiological recordings in rodents suggest that the long axis is organized along a gradient. Together, these observations suggest a model in which functional long-axis gradients are superimposed on discrete functional domains. This model provides a potential framework to explain and test the multiple functions ascribed to the hippocampus. }, + Author = {Strange, Bryan A and Witter, Menno P and Lein, Ed S and Moser, Edvard I}, + Date-Added = {2018-07-17 06:25:29 +0000}, + Date-Modified = {2018-07-17 06:25:29 +0000}, + Doi = {10.1038/nrn3785}, + Journal = {Nat Rev Neurosci}, + Journal-Full = {Nature reviews. Neuroscience}, + Mesh = {Animals; Gene Expression; Hippocampus; Humans}, + Month = {Oct}, + Number = {10}, + Pages = {655-69}, + Pmid = {25234264}, + Pst = {ppublish}, + Title = {Functional organization of the hippocampal longitudinal axis}, + Volume = {15}, + Year = {2014}, + File = {papers/Strange_NatRevNeurosci2014.pdf}, + Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn3785}} + +@article{Lisman:2017, + Author = {Lisman, John and Buzs{\'a}ki, Gy{\"o}rgy and Eichenbaum, Howard and Nadel, Lynn and Ranganath, Charan and Redish, A David}, + Date-Added = {2018-07-17 06:24:52 +0000}, + Date-Modified = {2018-07-17 06:24:52 +0000}, + Doi = {10.1038/nn.4661}, + Journal = {Nat Neurosci}, + Journal-Full = {Nature neuroscience}, + Month = {10}, + Number = {11}, + Pages = {1434-1447}, + Pmc = {PMC5943637}, + Pmid = {29073641}, + Pst = {ppublish}, + Title = {Viewpoints: how the hippocampus contributes to memory, navigation and cognition}, + Volume = {20}, + Year = {2017}, + File = {papers/Lisman_NatNeurosci2017.pdf}, + Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.4661}} + +@article{Cullen:2017, + Abstract = {In this Perspective, we evaluate current progress in understanding how the brain encodes our sense of direction, within the context of parallel work focused on how early vestibular pathways encode self-motion. In particular, we discuss how these systems work together and provide evidence that they involve common mechanisms. We first consider the classic view of the head direction cell and results of recent experiments in rodents and primates indicating that inputs to these neurons encode multimodal information during self-motion, such as proprioceptive and motor efference copy signals, including gaze-related information. We also consider the paradox that, while the head-direction network is generally assumed to generate a fixed representation of perceived directional heading, this computation would need to be dynamically updated when the relationship between voluntary motor command and its sensory consequences changes. Such situations include navigation in virtual reality and head-restricted conditions, since the natural relationship between visual and extravisual cues is altered.}, + Author = {Cullen, Kathleen E and Taube, Jeffrey S}, + Date-Added = {2018-07-17 06:23:49 +0000}, + Date-Modified = {2018-07-17 06:23:49 +0000}, + Doi = {10.1038/nn.4658}, + Journal = {Nat Neurosci}, + Journal-Full = {Nature neuroscience}, + Month = {Oct}, + Number = {11}, + Pages = {1465-1473}, + Pmid = {29073639}, + Pst = {aheadofprint}, + Title = {Our sense of direction: progress, controversies and challenges}, + Volume = {20}, + Year = {2017}, + File = {papers/Cullen_NatNeurosci2017.pdf}, + Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.4658}} + +@article{Moser:2017, + Abstract = {Since the first place cell was recorded and the cognitive-map theory was subsequently formulated, investigation of spatial representation in the hippocampal formation has evolved in stages. Early studies sought to verify the spatial nature of place cell activity and determine its sensory origin. A new epoch started with the discovery of head direction cells and the realization of the importance of angular and linear movement-integration in generating spatial maps. A third epoch began when investigators turned their attention to the entorhinal cortex, which led to the discovery of grid cells and border cells. This review will show how ideas about integration of self-motion cues have shaped our understanding of spatial representation in hippocampal-entorhinal systems from the 1970s until today. It is now possible to investigate how specialized cell types of these systems work together, and spatial mapping may become one of the first cognitive functions to be understood in mechanistic detail.}, + Author = {Moser, Edvard I and Moser, May-Britt and McNaughton, Bruce L}, + Date-Added = {2018-07-17 06:23:15 +0000}, + Date-Modified = {2018-07-17 06:23:15 +0000}, + Doi = {10.1038/nn.4653}, + Journal = {Nat Neurosci}, + Journal-Full = {Nature neuroscience}, + Mesh = {Action Potentials; Animals; Brain Mapping; Grid Cells; Hippocampus; Humans; Photic Stimulation; Space Perception}, + Month = {Oct}, + Number = {11}, + Pages = {1448-1464}, + Pmid = {29073644}, + Pst = {ppublish}, + Title = {Spatial representation in the hippocampal formation: a history}, + Volume = {20}, + Year = {2017}, + File = {papers/Moser_NatNeurosci2017.pdf}, + Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.4653}} + +@article{Kim:2014, + Abstract = {Larval zebrafish offer the potential for large-scale optical imaging of neural activity throughout the central nervous system; however, several barriers challenge their utility. First, ~panneuronal probe expression has to date only been demonstrated at early larval stages up to 7 days post-fertilization (dpf), precluding imaging at later time points when circuits are more mature. Second, nuclear exclusion of genetically-encoded calcium indicators (GECIs) limits the resolution of functional fluorescence signals collected during imaging. Here, we report the creation of transgenic zebrafish strains exhibiting robust, nuclearly targeted expression of GCaMP3 across the brain up to at least 14 dpf utilizing a previously described optimized Gal4-UAS system. We confirmed both nuclear targeting and functionality of the modified probe in vitro and measured its kinetics in response to action potentials (APs). We then demonstrated in vivo functionality of nuclear-localized GCaMP3 in transgenic zebrafish strains by identifying eye position-sensitive fluorescence fluctuations in caudal hindbrain neurons during spontaneous eye movements. Our methodological approach will facilitate studies of larval zebrafish circuitry by both improving resolution of functional Ca(2+) signals and by allowing brain-wide expression of improved GECIs, or potentially any probe, further into development. }, + Author = {Kim, Christina K and Miri, Andrew and Leung, Louis C and Berndt, Andre and Mourrain, Philippe and Tank, David W and Burdine, Rebecca D}, + Date-Added = {2018-07-16 22:03:08 +0000}, + Date-Modified = {2018-07-16 22:03:08 +0000}, + Doi = {10.3389/fncir.2014.00138}, + Journal = {Front Neural Circuits}, + Journal-Full = {Frontiers in neural circuits}, + Keywords = {brain-wide expression; genetically encoded calcium indicators; in vivo calcium imaging; nuclear calcium signals; transgenic zebrafish}, + Mesh = {Action Potentials; Animals; Animals, Genetically Modified; Brain; Brain Mapping; Cell Nucleus; Cells, Cultured; Eye Movements; Fluorescence; HEK293 Cells; Humans; Nerve Tissue Proteins; Neural Pathways; Neurons; Nuclear Proteins; Rats; Transfection; Zebrafish; Zebrafish Proteins}, + Pages = {138}, + Pmc = {PMC4244806}, + Pmid = {25505384}, + Pst = {epublish}, + Title = {Prolonged, brain-wide expression of nuclear-localized GCaMP3 for functional circuit mapping}, + Volume = {8}, + Year = {2014}, + File = {papers/Kim_FrontNeuralCircuits2014.pdf}} +