bentons crossing update

OMEGA.bib

@@ -948,7 +948,7 @@
 	Year = {2002},
 	url = {papers/Li_Neuron2002.pdf}}
 
-@article{Cuoco:2017,
+@article{Cuoco:2018,
 	Abstract = {C57BL/6 mice exhibit spontaneous cerebellar malformations consisting of heterotopic neurons and glia in the molecular layer of the posterior vermis, indicative of neuronal migration defect during cerebellar development. Recognizing that many genetically engineered (GE) mouse lines are produced from C57BL/6 ES cells or backcrossed to this strain, we performed histological analyses and found that cerebellar heterotopia were a common feature present in the majority of GE lines on this background. Furthermore, we identify GE mouse lines that will be valuable in the study of cerebellar malformations including diverse driver, reporter, and optogenetic lines. Finally, we discuss the implications that these data have on the use of C57BL/6 mice and GE mice on this background in studies of cerebellar development or as models of disease.},
 	Author = {Cuoco, Joshua A and Esposito, Anthony W and Moriarty, Shannon and Tang, Ying and Seth, Sonika and Toia, Alyssa R and Kampton, Elias B and Mayr, Yevgeniy and Khan, Mussarah and Khan, Mohammad B and Mullen, Brian R and Ackman, James B and Siddiqi, Faez and Wolfe, John H and Savinova, Olga V and Ramos, Raddy L},
 	Date-Added = {2018-01-19 23:05:48 +0000},
@@ -961,8 +961,8 @@
 	pmid = {29043563},
 	Pst = {aheadofprint},
 	Title = {Malformation of the Posterior Cerebellar Vermis Is a Common Neuroanatomical Phenotype of Genetically Engineered Mice on the C57BL/6 Background},
-	Year = {2017},
+	Year = {2018},
-	url = {papers/Cuoco_Cerebellum2017.pdf},
+	url = {papers/Cuoco_Cerebellum2018.pdf},
 	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s12311-017-0892-3}}
 
 @article{Murabe:1983,
@@ -9940,7 +9940,7 @@ VIDEO ABSTRACT: },
         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},
+        year = {2020},
         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.},
@@ -113784,3 +113784,572 @@ CONCLUSIONS: Centrifugal axons in the macaque retina are part of the system of a
   title = {Hands-On Machine Learning with Scikit-Learn and TensorFlow},
   year = {2017}
 }
+
+@article{Gribizis2019,
+  title = {Visual Cortex Gains Independence from Peripheral Drive before Eye Opening.},
+  author = {Gribizis, Alexandra and Ge, Xinxin and Daigle, Tanya L and Ackman, James B and Zeng, Hongkui and Lee, Daeyeol and Crair, Michael C},
+  journal = {Neuron},
+  volume = {104},
+  number = {4},
+  year = {2019},
+  month = {11},
+  pages = {711-723.e3},
+  abstract = {Visual spatial perception in the mammalian brain occurs through two parallel pathways: one reaches the primary visual cortex (V1) through the thalamus and another the superior colliculus (SC) via direct projections from the retina. The origin, development, and relative function of these two evolutionarily distinct pathways remain obscure. We examined the early functional development of both pathways by simultaneously imaging pre- and post-synaptic spontaneous neuronal activity. We observed that the quality of retinal activity transfer to the thalamus and superior colliculus does not change across the first two postnatal weeks. However, beginning in the second postnatal week, retinal activity does not drive V1 as strongly as earlier wave activity, suggesting that intrinsic cortical activity competes with signals from the sensory periphery as the cortex matures. Together, these findings bring new insight into the function of the SC and V1 and the role of peripheral activity in driving both circuits across development.},
+  keywords = {RCaMP; activity transfer; jRCaMP1b; lateral geniculate nucleus; retina; retinal waves; spontaneous activity; superior colliculus; visual cortex; visual system development; Animals; Female; Male; Mice, Inbred C57BL; Neurogenesis; Superior Colliculi; Visual Cortex; Visual Pathways; },
+  pmid = {31561919},
+  pii = {S0896-6273(19)30699-3},
+  doi = {10.1016/j.neuron.2019.08.015},
+  pmc = {PMC6872942},
+  mid = {NIHMS1539885},
+  url = {papers/Gribizis_Neuron2020-31561919.pdf},
+  nlmuniqueid = {8809320}
+}
+
+@article{Si2022,
+  title = {High-frequency hearing is required to compute a topographic map of auditory space in the mouse superior colliculus.},
+  author = {Si, Yufei and Ito, Shinya and Litke, Alan M and Feldheim, David A},
+  journal = {eNeuro},
+  year = {2022},
+  month = {Apr},
+  pages = {},
+  abstract = {A topographic map of auditory space is a feature found in the superior colliculus (SC) of many species, including CBA/CaJ mice. In this genetic background, high-frequency monaural spectral cues and interaural level differences are used to compute spatial receptive fields (RFs) that form a topographic map along the azimuth. Unfortunately, C57BL/6 mice, a strain widely used for transgenic manipulation, display age-related hearing loss (AHL) due to an inbred mutation in the Cadherin 23 gene (Cdh23) that affects hair cell mechanotransduction. To overcome this problem, researchers have used young C57BL/6 mice in their studies, as they have been shown to have normal hearing thresholds. However, important details of the auditory response characteristics of the SC such as spectral responses and spatial localization, have not been characterized in young C57BL/6 mice. Here we show that 2-4-month C57BL/6 mice lack neurons with frontal auditory RFs and therefore lack a topographic representation of auditory space in the SC. Analysis of the spectrotemporal receptive fields (STRFs) of the SC auditory neurons shows that C57BL/6 mouse SC neurons lack the ability to detect the high-frequency (>40kHz) spectral cues that are needed to compute frontal RFs. We also show that crossing C57BL/6 mice with CBA/CaJ mice or introducing one copy of the wild-type Cdh23 to C57BL/6 mice rescues the high-frequency hearing deficit and improves the topographic map of auditory space. Taken together, these results demonstrate the importance of high-frequency hearing in computing a topographic map of auditory space.Significance StatementDespite the strain's age-dependent hearing loss, C57BL/6 mice are widely used in auditory studies because of the development of transgenic reporter and Cre lines in this genetic background. Here we examined the topographic map of auditory space and spectrotemporal properties of neurons in the SC of C57BL/6 mice. We found an early-onset high-frequency hearing deficit that results in the loss of SC neurons with frontal RFs and, consequently, an absence of a topographic map of auditory space. These findings stress the importance of high-frequency hearing to compute spatially restricted receptive fields and serve as a caution to researchers that doing auditory-related research using the C57BL/6 genetic background may not be representative of true wild-type mice.},
+  pmid = {35473764},
+  pii = {ENEURO.0513-21.2022},
+  doi = {10.1523/ENEURO.0513-21.2022},
+  url = {papers/Si_eNeuro2022-35473764.pdf},
+  nlmuniqueid = {101647362}
+}
+
+@article{Song2022,
+  title = {Mesoscopic landscape of cortical functions revealed by through-skull wide-field optical imaging in marmoset monkeys.},
+  author = {Song, Xindong and Guo, Yueqi and Li, Hongbo and Chen, Chenggang and Lee, Jong Hoon and Zhang, Yang and Schmidt, Zachary and Wang, Xiaoqin},
+  journal = {Nat Commun},
+  volume = {13},
+  number = {1},
+  year = {2022},
+  month = {Apr},
+  pages = {2238},
+  abstract = {The primate cerebral cortex is organized into specialized areas representing different modalities and functions along a continuous surface. The functional maps across the cortex, however, are often investigated a single modality at a time (e.g., audition or vision). To advance our understanding of the complex landscape of primate cortical functions, here we develop a polarization-gated wide-field optical imaging method for measuring cortical functions through the un-thinned intact skull in awake marmoset monkeys (Callithrix jacchus), a primate species featuring a smooth cortex. Using this method, adjacent auditory, visual, and somatosensory cortices are noninvasively parcellated in individual subjects with detailed tonotopy, retinotopy, and somatotopy. An additional pure-tone-responsive tonotopic gradient is discovered in auditory cortex and a face-patch sensitive to motion in the lower-center visual field is localized near an auditory region representing frequencies of conspecific vocalizations. This through-skull landscape-mapping approach provides new opportunities for understanding how the primate cortex is organized and coordinated to enable real-world behaviors.},
+  keywords = {Animals; Auditory Cortex; Auditory Perception; Callithrix; Humans; Optical Imaging; Skull; },
+  pmid = {35474064},
+  doi = {10.1038/s41467-022-29864-7},
+  pii = {10.1038/s41467-022-29864-7},
+  pmc = {PMC9042927},
+  url = {papers/Song_NatCommun2022-35474064.pdf},
+  nlmuniqueid = {101528555}
+}
+
+
+@book{Allman1999,
+  author = {Allman, John Morgan},
+  isbn = {0-7167-5076-7},
+  publisher = {Scientific American Library},
+  title = {Evolving Brains},
+  year = {1999}
+}
+
+
+@book{Arey1954,
+  author = {Arey, Leslie Brainerd},
+  isbn = {54-6089},
+  publisher = {W.B. Saunders Company},
+  title = {Developmental Anatomy A Textbook and Laboratory Manual of Embryology},
+  year = {1954}
+}
+
+@book{Huettner1949,
+  author = {Huettner, Alfred F.},
+  publisher = {The Macmillan Company},
+  title = {Fundamentals of Comparative Embryology of the Vertebrates},
+  year = {1949}
+}
+
+@book{Asimov1966,
+  author = {Asimov, Issac},
+  isbn = {0-8802-9251-2},
+  publisher = {Barnes \& Nobel},
+  title = {Understanding Physics},
+  year = {1993}
+}
+
+@book{Aidley1989,
+  author = {Aidley, David J},
+  edition = {Third Edition},
+  isbn = {0-521-38863-5},
+  publisher = {Cambridge University Press},
+  title = {The Physiology of Excitable Cells},
+  year = {1989}
+}
+
+
+@book{Fowles1975,
+  author = {Fowles, Grant R},
+  edition = {Second Edition},
+  isbn = {978-0-486-65957-2},
+  publisher = {Dover},
+  title = {Introduction to Modern Optics},
+  year = {1989}
+}
+
+@book{Venables2002,
+  author = {Venables, WN and Ripley BD},
+  edition = {Fourth Edition},
+  isbn = {0-387-95457-0},
+  publisher = {Springer},
+  title = {Modern Applied Statistics with S},
+  year = {2002}
+}
+
+@book{Stark1970,
+  author = {Stark, Peter A},
+  isbn = {77-85773},
+  publisher = {Macmillan},
+  title = {Introduction to Numerical Methods},
+  year = {1970}
+}
+
+@book{Nowak2006,
+  author = {Nowak, Martin A},
+  isbn = {978-0-674-02338-3},
+  publisher = {Harvard},
+  title = {Evolutionary Dynamics: exploring the equations of life},
+  year = {2006}
+}
+
+@book{Tenenbaum1963,
+  author = {Tenenbaum, Morris and Pollard, Harry},
+  isbn = {978-0-674-02338-3},
+  publisher = {Dover},
+  title = {Ordinary Differential Equations},
+  year = {1985}
+}
+
+@book{Hille1984,
+  author = {Hille, Bertil},
+  isbn = {0-87893-322-0},
+  publisher = {Sinauer},
+  title = {Ionic Channels of Excitable Membranes},
+  year = {1984}
+}
+
+@book{Goodman1994,
+  author = {Goodman, H. Maurice},
+  isbn = {0-7817-0105-8},
+  edition = {Second Edition},
+  publisher = {Lippincott-Raven},
+  title = {Basic Medical Endocrinology},
+  year = {1994}
+}
+
+@book{Randall1997,
+  author = {Randall, David and Burggren, Warren and French, Kathleen},
+  isbn = {0-7167-2414-6},
+  edition = {Fourth Edition},
+  publisher = {W.H. Freeman and Company},
+  title = {Eckert Animal Physiology},
+  year = {1997}
+}
+
+@book{Greenspan2007,
+  author = {Greenspan, Ralph J},
+  isbn = {978-08796-9821-8},
+  edition = {Fourth Edition},
+  publisher = {Cold Spring Harbor Laboratory Press},
+  title = {An Introduction to Nervous Systems},
+  year = {2007}
+}
+
+@book{Purves2012,
+  author = {Purves, Dale and Augustine, George J and Fitzpatrick, David and Hall, William C and LaMantia, Anthony-Samuel and White, Leonard E},
+  isbn = {978-0-87893-695-3},
+  edition = {Fifth Edition},
+  publisher = {Sinauer},
+  title = {Neuroscience},
+  year = {2012}
+}
+
+@book{Newman2013,
+  author = {Newman, Mark},
+  isbn = {978-148014551-1},
+  title = {Computational Physics},
+  year = {2013}
+}
+
+@book{Strogatz2015,
+  author = {Strogatz, Steven},
+  isbn = {978-0-8133-4910-7},
+  publisher = {Westview Press},
+  title = {Nonlinear Dynamics and Chaos},
+  year = {2015}
+}
+
+@book{Mendelson1990,
+  author = {Mendelson, Bert},
+  isbn = {0-312-04123-3},
+  edition = {Third Edition},
+  publisher = {Dover},
+  title = {Introduction to Topology},
+  year = {1990}
+}
+
+@book{Anton1995,
+  author = {Anton, Howard},
+  isbn = {0-471-59495-4},
+  edition = {Fifth Edition},
+  publisher = {Wiley},
+  title = {Calculus with Analytic Geometry},
+  year = {1995}
+}
+
+@book{Strang2016,
+  author = {Strang, Gilbert},
+  isbn = {978-0-9802327-7-6},
+  edition = {Fifth Edition},
+  publisher = {Wellesey-Cambridge Press},
+  title = {Introduction to Linear Algebra},
+  year = {2016}
+}
+
+@book{Brown1993,
+  author = {Brown, D and Rothery, P},
+  isbn = {0-471-93322-8},
+  publisher = {Wiley},
+  title = {Models in Biology: Mathematics, Statistics and Computing},
+  year = {1993}
+}
+
+@book{Dayan2001,
+  author = {Dayan, Peter and Abbot, Larry F},
+  isbn = {978-0-262-54185-5},
+  publisher = {MIT Press},
+  title = {Theoretical Neuroscience},
+  year = {2001}
+}
+
+@book{Pierce1980,
+  author = {Pierce, John R},
+  isbn = {978-0-486-24061-9},
+  edition = {Second Edition},
+  publisher = {Dover},
+  title = {An Introduciton to Information Theory},
+  year = {1980}
+}
+
+@book{Rieke1999,
+  author = {Rieke, Fred and Warland, David and Steveninck, Rob de Ruyter and Bialek, William},
+  isbn = {978-0-262-68108-7},
+  publisher = {MIT Press},
+  title = {Spikes : Exploring the Neural Code},
+  year = {1999}
+}
+
+@book{Swanson2003,
+  author = {Swanson, Larry W},
+  isbn = {0-19-510504-4},
+  publisher = {Oxford Univeristy Press},
+  title = {Brain Architecture : Understanding the Basic Plan},
+  year = {2003}
+}
+
+@book{Pickover1990,
+  author = {Pickover, Clifford A},
+  isbn = {0-312-04123-3},
+  publisher = {St Martin's Press},
+  title = {Computers, Pattern, Chaos, and Beauty},
+  year = {1990}
+}
+
+@book{Grus2015,
+  author = {Grus, Joel},
+  isbn = {978-1-491-90142-7},
+  publisher = {O'Reilly},
+  title = {Data Science from Scratch},
+  year = {2015}
+}
+
+@book{Shankar1995,
+  author = {Shankar, R},
+  isbn = {0-306-45036-4},
+  publisher = {Plenum},
+  title = {Basic Training in Mathematics : A Fitness Program for Science Students},
+  year = {1995}
+}
+
+@book{Calvin1998,
+  author = {Calvin, William H},
+  isbn = {9780262531542},
+  publisher = {MIT Press},
+  title = {The Cerebral Code : Thinking a Though in the Mosaics of the Mind},
+  year = {1998}
+}
+
+@book{Kandel2000,
+  author = {Kandel, Eric and Schwartz, James H and Jessell, Thomas M},
+  isbn = {0-8385-7701-6},
+  publisher = {McGraw-Hill},
+  title = {Principles of Neural Science},
+  edition = {Fourth Edition},
+  year = {2000}
+}
+
+@book{Siegel1999,
+  author = {Siegel, George J and Agranoff, Bernard W and Albers, R. Wayne and Fisher, Stephen K and Uhler, Michael D},
+  isbn = {0-397-51820-X},
+  publisher = {Lippincott Williams \& Wilkins},
+  title = {Basic Neurochemistry},
+  edition = {Sixth Edition},
+  year = {1999}
+}
+
+@book{Luo2016,
+  author = {Luo, Liqun},
+  isbn = {978-0-8153-4494-0},
+  publisher = {Garland Science},
+  title = {Principles of Neurobiolgy},
+  year = {2016}
+}
+
+@book{Axon1993,
+  editor = {Sherman-Gold, Rivka},
+  publisher = {Axon Instruments},
+  title = {The Axon Guide for Electrophysiology \& Biophysics Laboratory Techniques},
+  year = {1993}
+}
+
+@book{DeFelipe1988,
+  editor = {Defelipe, Javier and Jones, Edward G},
+  isbn = {0-19-505280-3},
+  publisher = {Oxford University Press},
+  title = {Cajal On The Cerebral Cortex : An Annotated Translation of the Complete Writings},
+  year = {1988}
+}
+
+@book{Shepherd2004,
+  editor = {Shepherd, Gordon M},
+  isbn = {978-0-19-515965-1},
+  publisher = {Oxford University Press},
+  title = {The Synaptic Organization of the Brain},
+  edition = {Fifth Edition},
+  year = {2004}
+}
+
+@book{Chatfield2004,
+  author = {Chatfield, Christopher},
+  isbn = {1-58488-317-0},
+  publisher = {CRC Press},
+  title = {The Analysis of Time Series : an introduction},
+  edition = {Sixth Edition},
+  year = {2004}
+}
+
+@book{Tufte2001,
+  author = {Tufte, Edward R},
+  publisher = {Graphics Press},
+  title = {The Visual Display of Quantitative Information},
+  edition = {Second Edition},
+  year = {2001}
+}
+
+@book{Buzsáki2006,
+  author = {Buzsáki, György},
+  isbn = {978-0-19-530106-9},
+  publisher = {Oxford University Press},
+  title = {Rhythms of the Brain},
+  year = {2006}
+}
+
+@book{Mitra2008,
+  author = {Mitra, Partha P and Bokil, Hemant},
+  isbn = {978-0-19-517808-1},
+  publisher = {Oxford University Press},
+  title = {Observed Brain Dynamics},
+  year = {2008}
+}
+
+@book{Daw2006,
+  author = {Daw, Nigel W},
+  isbn = {978-0387-25371-8},
+  publisher = {Springer},
+  title = {Visual Development},
+  edition = {Second Edition},
+  year = {2006}
+}
+
+@book{Anderson2012,
+  author = {Anderson, Chris},
+  isbn = {978-0-307-72096-2},
+  publisher = {Crown},
+  title = {Makers : The New Industrial Revolution},
+  year = {2012}
+}
+
+@book{Dalgaard2008,
+  author = {Dalgaard, Peter},
+  isbn = {978-0-387-79053-4},
+  publisher = {Springer},
+  title = {Introductory Statistics with R},
+  edition = {Second Edition},
+  year = {2008}
+}
+
+@book{Cajal1999,
+  author = {Cajal, Santiago Ramón y},
+  isbn = {0-262-68150-1},
+  publisher = {MIT},
+  title = {Advice For a Young Investigator},
+  year = {1999}
+}
+
+@book{Yuste2000,
+  editor = {Yuste, Rafael and Lanni, Frederick and Konnerth, Arthur},
+  isbn = {0-87969-542-0},
+  publisher = {Coold Spring Harbor Laboratory Press},
+  title = {Imaging Neurons},
+  year = {2000}
+}
+
+@book{Gonzalez2009,
+  author = {Gonzalez, Rafael C and Woods, Richard E and Eddins, Steven L},
+  isbn = {978-0-9820854-0-0},
+  publisher = {Gatesmark},
+  title = {Digital Image Processing Using MATLAB},
+  edition = {Second Edition},
+  year = {2009}
+}
+
+@book{Bradski2008,
+  author = {Bradski, Gary and Kaehler, Adrian},
+  isbn = {978-0-596-51613-0},
+  publisher = {O'Reilly},
+  title = {Learning OpenCV},
+  year = {2008}
+}
+
+@book{Pawley2006,
+  editor = {Pawley, James B},
+  isbn = {987-0-387-25921-5},
+  publisher = {Springer},
+  title = {Handbook of Biological Confocal Microscopy},
+  edition = {Third Edition},
+  year = {2008}
+}
+
+@book{Fields1996,
+  editor = {Fields, Bernard N and Knipe, David M and Howley, Peter M},
+  isbn = {0-7817-0284-4},
+  publisher = {Lippincott-Raven},
+  title = {Fundamental Virology},
+  edition = {Third Edition},
+  year = {1996}
+}
+
+@book{Wrede1963,
+  author = {Wrede, Robert C},
+  isbn = {63-20645},
+  publisher = {Wiley},
+  title = {Introduction to Vector and Tensor Analysis},
+  year = {1963}
+}
+
+@book{Collin1990,
+  author = {Collin, Robert E},
+  isbn = {0-87942-237-8},
+  publisher = {IEEE Press},
+  edition = {Second Edition},
+  title = {Field Theory of Guided Waves},
+  year = {1990}
+}
+
+@article{Atasoy2016,
+  title = {Human brain networks function in connectome-specific harmonic waves.},
+  author = {Atasoy, Selen and Donnelly, Isaac and Pearson, Joel},
+  journal = {Nat Commun},
+  volume = {7},
+  year = {2016},
+  month = {Jan},
+  pages = {10340},
+  abstract = {A key characteristic of human brain activity is coherent, spatially distributed oscillations forming behaviour-dependent brain networks. However, a fundamental principle underlying these networks remains unknown. Here we report that functional networks of the human brain are predicted by harmonic patterns, ubiquitous throughout nature, steered by the anatomy of the human cerebral cortex, the human connectome. We introduce a new technique extending the Fourier basis to the human connectome. In this new frequency-specific representation of cortical activity, that we call 'connectome harmonics', oscillatory networks of the human brain at rest match harmonic wave patterns of certain frequencies. We demonstrate a neural mechanism behind the self-organization of connectome harmonics with a continuous neural field model of excitatory-inhibitory interactions on the connectome. Remarkably, the critical relation between the neural field patterns and the delicate excitation-inhibition balance fits the neurophysiological changes observed during the loss and recovery of consciousness. },
+  keywords = {Adult; Brain; Brain Mapping; Connectome; Female; Humans; Male; Nerve Net; Young Adult; },
+  pmid = {26792267},
+  pii = {ncomms10340},
+  doi = {10.1038/ncomms10340},
+  pmc = {PMC4735826},
+  url = {papers/Atasoy_NatCommun2016-26792267.pdf},
+  nlmuniqueid = {101528555}
+}
+
+@article{Barabási2020,
+  title = {A Genetic Model of the Connectome.},
+  author = {Barabási, Dániel L and Barabási, Albert-László},
+  journal = {Neuron},
+  volume = {105},
+  number = {3},
+  year = {2020},
+  month = {02},
+  pages = {435-445.e5},
+  abstract = {The connectomes of organisms of the same species show remarkable architectural and often local wiring similarity, raising the question: where and how is neuronal connectivity encoded? Here, we start from the hypothesis that the genetic identity of neurons guides synapse and gap-junction formation and show that such genetically driven wiring predicts the existence of specific biclique motifs in the connectome. We identify a family of large, statistically significant biclique subgraphs in the connectomes of three species and show that within many of the observed bicliques the neurons share statistically significant expression patterns and morphological characteristics, supporting our expectation of common genetic factors that drive the synapse formation within these subgraphs. The proposed connectome model offers a self-consistent framework to link the genetics of an organism to the reproducible architecture of its connectome, offering experimentally falsifiable predictions on the genetic factors that drive the formation of individual neuronal circuits.},
+  keywords = {Brain Networks; C. elegans; Connectomics; Generative Model; Theory; development; encoding; Animals; Brain; Caenorhabditis elegans; Ciona intestinalis; Connectome; Drosophila; Models, Genetic; Nerve Net; },
+  pmid = {31806491},
+  pii = {S0896-6273(19)30926-2},
+  doi = {10.1016/j.neuron.2019.10.031},
+  pmc = {PMC7007360},
+  mid = {NIHMS1543676},
+  url = {papers/Barabási_Neuron2020-31806491.pdf},
+  nlmuniqueid = {8809320}
+}
+
+@article{Cheng2022,
+  title = {Vision-dependent specification of cell types and function in the developing cortex.},
+  author = {Cheng, Sarah and Butrus, Salwan and Tan, Liming and Xu, Runzhe and Sagireddy, Srikant and Trachtenberg, Joshua T and Shekhar, Karthik and Zipursky, S Lawrence},
+  journal = {Cell},
+  volume = {185},
+  number = {2},
+  year = {2022},
+  month = {01},
+  pages = {311-327.e24},
+  abstract = {The role of postnatal experience in sculpting cortical circuitry, while long appreciated, is poorly understood at the level of cell types. We explore this in the mouse primary visual cortex (V1) using single-nucleus RNA sequencing, visual deprivation, genetics, and functional imaging. We find that vision selectively drives the specification of glutamatergic cell types in upper layers (L) (L2/3/4), while deeper-layer glutamatergic, GABAergic, and non-neuronal cell types are established prior to eye opening. L2/3 cell types form an experience-dependent spatial continuum defined by the graded expression of ∼200 genes, including regulators of cell adhesion and synapse formation. One of these genes, Igsf9b, a vision-dependent gene encoding an inhibitory synaptic cell adhesion molecule, is required for the normal development of binocular responses in L2/3. In summary, vision preferentially regulates the development of upper-layer glutamatergic cell types through the regulation of cell-type-specific gene expression programs.},
+  keywords = {binocular vision; cell types; critical period; inhibitory synapses; layer 2/3; single-nucleus RNA-seq; visual cortex; Animals; Animals, Newborn; Biomarkers; Gene Expression Profiling; Gene Expression Regulation, Developmental; Glutamic Acid; Male; Membrane Proteins; Mice, Inbred C57BL; Nerve Tissue Proteins; Neurons; RNA-Seq; Transcriptome; Vision, Binocular; Vision, Ocular; Visual Cortex; gamma-Aminobutyric Acid; },
+  pmid = {35063073},
+  pii = {S0092-8674(21)01485-9},
+  doi = {10.1016/j.cell.2021.12.022},
+  pmc = {PMC8813006},
+  mid = {NIHMS1770258},
+  url = {papers/Cheng_Cell2022-35063073.pdf},
+  nlmuniqueid = {0413066}
+}
+
+@article{Bajar2022,
+  title = {A discrete neuronal population coordinates brain-wide developmental activity.},
+  author = {Bajar, Bryce T and Phi, Nguyen T and Isaacman-Beck, Jesse and Reichl, Jun and Randhawa, Harpreet and Akin, Orkun},
+  journal = {Nature},
+  volume = {602},
+  number = {7898},
+  year = {2022},
+  month = {02},
+  pages = {639-646},
+  abstract = {In vertebrates, stimulus-independent activity accompanies neural circuit maturation throughout the developing brain1,2. The recent discovery of similar activity in the developing Drosophila central nervous system suggests that developmental activity is fundamental to the assembly of complex brains3. How such activity is coordinated across disparate brain regions to influence synaptic development at the level of defined cell types is not well understood. Here we show that neurons expressing the cation channel transient receptor potential gamma (Trpγ) relay and pattern developmental activity throughout the Drosophila brain. In trpγ mutants, activity is attenuated globally, and both patterns of activity and synapse structure are altered in a cell-type-specific manner. Less than 2% of the neurons in the brain express Trpγ. These neurons arborize throughout the brain, and silencing or activating them leads to loss or gain of brain-wide activity. Together, these results indicate that this small population of neurons coordinates brain-wide developmental activity. We propose that stereotyped patterns of developmental activity are driven by a discrete, genetically specified network to instruct neural circuit assembly at the level of individual cells and synapses. This work establishes the fly brain as an experimentally tractable system for studying how activity contributes to synapse and circuit formation.},
+  keywords = {Animals; Brain; Drosophila; Neurogenesis; Neurons; Synapses; },
+  pmid = {35140397},
+  doi = {10.1038/s41586-022-04406-9},
+  pii = {10.1038/s41586-022-04406-9},
+  pmc = {PMC9020639},
+  mid = {NIHMS1792721},
+  url = {papers/Bajar_Nature2022-35140397.pdf},
+  nlmuniqueid = {0410462}
+}
+
+@article{Cossart2022,
+  title = {Step by step: cells with multiple functions in cortical circuit assembly.},
+  author = {Cossart, Rosa and Garel, Sonia},
+  journal = {Nat Rev Neurosci},
+  year = {2022},
+  month = {Apr},
+  pages = {},
+  abstract = {It is often thought that the construction of cortical circuits occurs as the result of an elegantly designed process that unfolds sequentially as an animal develops until adult functional networks emerge. In reality, cortical circuits are shaped by evolutionary mechanisms, changes in developmental programmes driven by neuronal activity or epigenetic mechanisms and the need to adapt to the external world, and must pass through several important phases and timely checkpoints as they form. Some cortical cell types serve multiple functions during this developmental journey and are then reused (or 'recycled') to perform different functions in the adult cortex. Understanding the different stages of the cortical construction process and taking into account the ways in which cellular functions change across time and space is therefore essential if we are to build a comprehensive framework of cortical wiring in both health and disease.},
+  pmid = {35422526},
+  doi = {10.1038/s41583-022-00585-6},
+  pii = {10.1038/s41583-022-00585-6},
+  url = {papers/Cossart_NatRevNeurosci2022-35422526.pdf},
+  nlmuniqueid = {100962781}
+}
+

bibd-md.csl

@@ -306,7 +306,7 @@
       <text variable="citation-number"/>
     </layout>
   </citation>
-  <bibliography et-al-min="7" et-al-use-first="6" second-field-align="flush">
+  <bibliography et-al-min="17" et-al-use-first="6" second-field-align="flush">
     <layout>
         <text macro="access-id" prefix="[^" suffix="]: "/>
       <group delimiter=". " suffix=". ">