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OMEGA.bib

@@ -111461,3 +111461,146 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
   nlmuniqueid = {0266262}
 }
 
+@article{Kaschube2010,
+  title = {Universality in the evolution of orientation columns in the visual cortex.},
+  author = {Kaschube, Matthias and Schnabel, Michael and Löwel, Siegrid and Coppola, David M and White, Leonard E and Wolf, Fred},
+  journal = {Science},
+  volume = {330},
+  number = {6007},
+  year = {2010},
+  month = {Nov},
+  pages = {1113-6},
+  abstract = {The brain's visual cortex processes information concerning form, pattern, and motion within functional maps that reflect the layout of neuronal circuits. We analyzed functional maps of orientation preference in the ferret, tree shrew, and galago--three species separated since the basal radiation of placental mammals more than 65 million years ago--and found a common organizing principle. A symmetry-based class of models for the self-organization of cortical networks predicts all essential features of the layout of these neuronal circuits, but only if suppressive long-range interactions dominate development. We show mathematically that orientation-selective long-range connectivity can mediate the required interactions. Our results suggest that self-organization has canalized the evolution of the neuronal circuitry underlying orientation preference maps into a single common design.},
+  pubmed = {21051599},
+  pii = {science.1194869},
+  doi = {10.1126/science.1194869},
+  pmc = {PMC3138194},
+  mid = {NIHMS302162},
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/21051599},
+  file = {papers/Kaschube_Science2010-21051599.pdf},
+  nlmuniqueid = {0404511}
+}
+
+@article{Reimann2017,
+  title = {Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function.},
+  author = {Reimann, Michael W and Nolte, Max and Scolamiero, Martina and Turner, Katharine and Perin, Rodrigo and Chindemi, Giuseppe and Dłotko, Paweł and Levi, Ran and Hess, Kathryn and Markram, Henry},
+  journal = {Front Comput Neurosci},
+  volume = {11},
+  year = {2017},
+  pages = {48},
+  abstract = {The lack of a formal link between neural network structure and its emergent function has hampered our understanding of how the brain processes information. We have now come closer to describing such a link by taking the direction of synaptic transmission into account, constructing graphs of a network that reflect the direction of information flow, and analyzing these directed graphs using algebraic topology. Applying this approach to a local network of neurons in the neocortex revealed a remarkably intricate and previously unseen topology of synaptic connectivity. The synaptic network contains an abundance of cliques of neurons bound into cavities that guide the emergence of correlated activity. In response to stimuli, correlated activity binds synaptically connected neurons into functional cliques and cavities that evolve in a stereotypical sequence toward peak complexity. We propose that the brain processes stimuli by forming increasingly complex functional cliques and cavities.},
+  keywords = {Betti numbers; connectomics; correlations; directed networks; structure-function; topology; },
+  pubmed = {28659782},
+  doi = {10.3389/fncom.2017.00048},
+  pmc = {PMC5467434},
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/28659782},
+  file = {},
+  nlmuniqueid = {101477956}
+}
+
+@article{Fongang2013,
+  title = {The precise timeline of transcriptional regulation reveals causation in mouse somitogenesis network.},
+  author = {Fongang, Bernard and Kudlicki, Andrzej},
+  journal = {BMC Dev Biol},
+  volume = {13},
+  year = {2013},
+  month = {Dec},
+  pages = {42},
+  abstract = {In vertebrate development, the segmental pattern of the body axis is established as somites, masses of mesoderm distributed along the two sides of the neural tube, are formed sequentially in the anterior-posterior axis. This mechanism depends on waves of gene expression associated with the Notch, Fgf and Wnt pathways. The underlying transcriptional regulation has been studied by whole-transcriptome mRNA profiling; however, interpretation of the results is limited by poor resolution, noisy data, small sample size and by the absence of a wall clock to assign exact time for recorded points.},
+  pubmed = {24304493},
+  pii = {1471-213X-13-42},
+  doi = {10.1186/1471-213X-13-42},
+  pmc = {PMC4235037},
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/24304493},
+  file = {papers/Fongang_BMCDevBiol2013-24304493.pdf},
+  nlmuniqueid = {100966973}
+}
+
+@article{Dequéant2006,
+  title = {A complex oscillating network of signaling genes underlies the mouse segmentation clock.},
+  author = {Dequéant, Mary-Lee and Glynn, Earl and Gaudenz, Karin and Wahl, Matthias and Chen, Jie and Mushegian, Arcady and Pourquié, Olivier},
+  journal = {Science},
+  volume = {314},
+  number = {5805},
+  year = {2006},
+  month = {Dec},
+  pages = {1595-8},
+  abstract = {The segmental pattern of the spine is established early in development, when the vertebral precursors, the somites, are rhythmically produced from the presomitic mesoderm. Microarray studies of the mouse presomitic mesoderm transcriptome reveal that the oscillator associated with this process, the segmentation clock, drives the periodic expression of a large network of cyclic genes involved in cell signaling. Mutually exclusive activation of the notch-fibroblast growth factor and Wnt pathways during each cycle suggests that coordinated regulation of these three pathways underlies the clock oscillator.},
+  pubmed = {17095659},
+  pii = {1133141},
+  doi = {10.1126/science.1133141},
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/17095659},
+  file = {papers/Dequéant_Science2006-17095659.pdf},
+  nlmuniqueid = {0404511}
+}
+
+@article{Aulehla2006,
+  title = {On periodicity and directionality of somitogenesis.},
+  author = {Aulehla, Alexander and Pourquié, Olivier},
+  journal = {Anat Embryol (Berl)},
+  volume = {211 Suppl 1},
+  year = {2006},
+  month = {Dec},
+  pages = {3-8},
+  abstract = {It is currently thought that the mechanism underlying somitogenesis is linked to a molecular oscillator, the segmentation clock, and to gradients of signaling molecules within the paraxial mesoderm. Here, we review the current picture of this segmentation clock and gradients, and use this knowledge to critically ask: What is the basis for periodicity and directionality of somitogenesis?},
+  pubmed = {17024300},
+  doi = {10.1007/s00429-006-0124-y},
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/17024300},
+  file = {papers/Aulehla_AnatEmbryol(Berl)2006-17024300.pdf},
+  nlmuniqueid = {7505194}
+}
+
+@article{Pittendrigh1954,
+  title = {ON TEMPERATURE INDEPENDENCE IN THE CLOCK SYSTEM CONTROLLING EMERGENCE TIME IN DROSOPHILA.},
+  author = {Pittendrigh, C S},
+  journal = {Proc Natl Acad Sci U S A},
+  volume = {40},
+  number = {10},
+  year = {1954},
+  month = {Oct},
+  pages = {1018-29},
+  pubmed = {16589583},
+  pmc = {PMC534216},
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/16589583},
+  file = {papers/Pittendrigh_ProcNatlAcadSciUSA1954-16589583.pdf},
+  nlmuniqueid = {7505876}
+}
+
+@article{Mizuno2018,
+  title = {Patchwork-Type Spontaneous Activity in Neonatal Barrel Cortex Layer 4 Transmitted via Thalamocortical Projections.},
+  author = {Mizuno, Hidenobu and Ikezoe, Koji and Nakazawa, Shingo and Sato, Takuya and Kitamura, Kazuo and Iwasato, Takuji},
+  journal = {Cell Rep},
+  volume = {22},
+  number = {1},
+  year = {2018},
+  month = {Jan},
+  pages = {123-135},
+  abstract = {Establishment of precise neuronal connectivity in the neocortex relies on activity-dependent circuit reorganization during postnatal development; however, the nature of cortical activity during this period remains largely unknown. Using two-photon calcium imaging of the barrel cortex in vivo during the first postnatal week, we reveal that layer 4 (L4) neurons within the same barrel fire synchronously in the absence of peripheral stimulation, creating a "patchwork" pattern of spontaneous activity corresponding to the barrel map. By generating transgenic mice expressing GCaMP6s in thalamocortical axons, we show that thalamocortical axons also demonstrate the spontaneous patchwork activity pattern. Patchwork activity is diminished by peripheral anesthesia but is mostly independent of self-generated whisker movements. The patchwork activity pattern largely disappeared during postnatal week 2, as even L4 neurons within the same barrel tended to fire asynchronously. This spontaneous L4 activity pattern has features suitable for thalamocortical (TC) circuit refinement in the neonatal barrel cortex.},
+  keywords = {activity-dependent development; awake; barrel cortex; in vivo calcium imaging; neonates; single-cell labeling; spontaneous activity; synchronized activity; thalamocortical axons; whisker monitoring; },
+  pubmed = {29298415},
+  pii = {S2211-1247(17)31808-9},
+  doi = {10.1016/j.celrep.2017.12.012},
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/29298415},
+  file = {papers/Mizuno_CellRep2018-29298415.pdf},
+  nlmuniqueid = {101573691}
+}
+
+@article{Petersen2007,
+  title = {The functional organization of the barrel cortex.},
+  author = {Petersen, Carl C H},
+  journal = {Neuron},
+  volume = {56},
+  number = {2},
+  year = {2007},
+  month = {Oct},
+  pages = {339-55},
+  abstract = {The tactile somatosensory pathway from whisker to cortex in rodents provides a well-defined system for exploring the link between molecular mechanisms, synaptic circuits, and behavior. The primary somatosensory cortex has an exquisite somatotopic map where each individual whisker is represented in a discrete anatomical unit, the "barrel," allowing precise delineation of functional organization, development, and plasticity. Sensory information is actively acquired in awake behaving rodents and processed differently within the barrel map depending upon whisker-related behavior. The prominence of state-dependent cortical sensory processing is likely to be crucial in our understanding of active sensory perception, experience-dependent plasticity and learning.},
+  pubmed = {17964250},
+  pii = {S0896-6273(07)00715-5},
+  doi = {10.1016/j.neuron.2007.09.017},
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/17964250},
+  file = {papers/Petersen_Neuron2007-17964250.pdf},
+  nlmuniqueid = {8809320}
+}
+
+@Comment{jabref-meta: databaseType:bibtex;}