Friday Paper List – Posted Saturday September 28th

boop. BOINK

Papers below:

1) Cocaine Disinhibits Dopamine Neurons by Potentiation of GABA Transmission in the Ventral Tegmental Area Christina Bocklisch, Vincent Pascoli, Jovi C. Y. Wong, David R. C. House, Cédric Yvon, Mathias de Roo, Kelly R. Tan, Christian Lüscher ; Science 2013 (link)

2) The Inhibitory Circuit Architecture of the Lateral Hypothalamus Orchestrates Feeding Joshua H. Jennings, Giorgio Rizzi, Alice M. Stamatakis, Randall L. Ung, Garret D. Stuber ; Science 2013 (link)

3) Robotic Leg Control with EMG Decoding in an Amputee with Nerve Transfers Levi J. Hargrove, Ph.D., Ann M. Simon, Ph.D., Aaron J. Young, M.S., Robert D. Lipschutz, C.P., Suzanne B. Finucane, M.S., Douglas G. Smith, M.D., and Todd A. Kuiken, M.D., Ph.D. ; The New England Journal of Medicine 2013 (link)

4) Shared Representations for Working Memory and Mental Imagery in Early Visual Cortex Anke Marit Albers, Peter Kok, Ivan Toni, H. Chris Dijkerman, and Floris P. de Lange ; Current Biology 2013 (link)

  • Imagery and visual working memory: one and the same? Frank Tong ; Trends in Cognitive Sciences 2013 (link)

5) Hippocampus-Dependent Strengthening of Targeted Memories via Reactivation during Sleep in Humans Lluıs Fuentemilla, Julia Miro, Pablo Ripolles, Adria` Vila`-Ballo, Montserrat Juncadella, Sara Castaner, Neus Salord, Carmen Monasterio, Merce` Falip, and Antoni Rodrıguez-Fornells ; Current Biology 2013 (link)

  • Memory Processing: The Critical Role of Neuronal Replay during Sleep Jocelyn Breton and Edwin M. Robertson ; Current Biology 2013 (link)

6) Cellular, columnar and modular organization of spatial representations in medial entorhinal cortex Andrea Burgalossi and Michael Brecht ; Current Opinion in Neurobiology 2013 (link)

7) A mouse model of higher visual cortical function Lindsey L Glickfeld, R Clay Reid and Mark L Andermann ; Current Opinion in Neurobiology 2013 (link)

8) Microcircuit dynamics of map plasticity in barrel cortex David J Margolis, Henry Lutcke and Fritjof Helmchen ; Current Opinion in Neurobiology 2013 (link)

9) Motor maps and the cortical control of movement Thomas C Harrison and Timothy H Murphy ; Current Opinion in Neurobiology 2013 (link)

10) Spontaneous cortical activity alternates between motifs defined by regional axonal projections Majid H Mohajerani, Allen W Chan, Mostafa Mohsenvand, Jeffrey LeDue, Rui Liu, David A McVea, Jamie D Boyd, Yu Tian Wang, Mark Reimers & Timothy H Murphy ; Nature Neuroscience 2013 (link)

11) Multiple perceptible signals from a single olfactory glomerulus Matthew Smear, Admir Resulaj, Jingji Zhang, Thomas Bozza & Dmitry Rinberg ; Nature Neuroscience 2013 (link)

12) Optogenetic identification of a rapid eye movement sleep modulatory circuit in the hypothalamus Sonia Jego, Stephen D Glasgow, Carolina Gutierrez Herrera, Mats Ekstrand, Sean J Reed, Richard Boyce, Jeffrey Friedman, Denis Burdakov & Antoine R Adamantidis ; Nature Neuroscience 2013 (link)

13) The Basal Ganglia Is Necessary for Learning Spectral, but Not Temporal, Features of Birdsong Farhan Ali, Timothy M. Otchy, Cengiz Pehlevan, Antoniu L. Fantana, Yoram Burak, and Bence P. O lveczky ; Neuron 2013 (link)

14) Nanoscale-Targeted Patch-Clamp Recordings of Functional Presynaptic Ion Channels Pavel Novak, Julia Gorelik, Umesh Vivekananda, Andrew I. Shevchuk, Yaroslav S. Ermolyuk, Russell J. Bailey, Andrew J. Bushby, Guy W.J. Moss, Dmitri A. Rusakov, David Klenerman, Dimitri M. Kullmann, Kirill E. Volynski, and Yuri E. Korchev ; Neuron 2013 (link)

15) Coding of Object Location in the Vibrissal Thalamocortical System Chunxiu Yu, Guy Horev, Naama Rubin, Dori Derdikman, Sebastian Haidarliu and Ehud Ahissar ; Cerebral Cortex 2013 (link)

16) Indirection and symbol-like processing in the prefrontal cortex and basal ganglia Trenton Krietea, David C. Noelleb, Jonathan D. Cohenc, and Randall C. O’Reilly ; PNAS 2013 (link)

17) Short-term synaptic plasticity in the deterministic Tsodyks–Markram model leads to unpredictable network dynamics Jesus M. Cortes, Mathieu Desroches, Serafim Rodrigues, Romain Veltz, Miguel A. Muñoz, and Terrence J. Sejnowski ; PNAS 2013 (link)

18) Presynaptic gating of excitation in the dorsal raphe nucleus by GABA Mariano Soiza-Reilly, Wayne B. Anderson, Christopher W. Vaughan, and Kathryn G. Commons ; PNAS 2013 (link)

19) Clusters of cerebellar Purkinje cells control their afferent climbing fiber discharge Joseph Chaumont, Nicolas Guyon, Antoine M. Valera, Guillaume P. Dugué, Daniela Popa, Paikan Marcaggi, Vanessa Gautheron, Sophie Reibel-Foisset, Stéphane Dieudonné, Aline Stephan, Michel Barrot, Jean-Christophe Cassel, Jean-Luc Dupont, Frédéric Doussau, Bernard Poulain, Fekrije Selimi, Clément Léna, and Philippe Isope ; PNAS 2013 (link)

20) Brain Systems for Probabilistic and Dynamic Prediction: Computational Specificity and Integration Jill X. O’Reilly, Saad Jbabdi, Matthew F. S. Rushworth, Timothy E. J. Behrens ; PLoS Biology 2013 (link)

21) Physical Principles for Scalable Neural Recording  Adam H. Marblestone, Bradley M. Zamft, Yael G. Maguire, Mikhail G. Shapiro, Thaddeus R. Cybulski, Joshua I. Glaser, Dario Amodei, P. Benjamin Stranges, Reza Kalhor, David A. Dalrymple, Dongjin Seo, Elad Alon, Michel M. Maharbiz, Jose M. Carmena, Jan M. Rabaey, Edward S. Boyden, George M. Church, and Konrad P. Kording ; Frontiers in Computational Neuroscience 2013 (link)

22) Opposite Adaptive Processing of Stimulus Intensity in Two Major Nuclei of the Somatosensory Brainstem Boaz Mohar, Yonatan Katz, and Ilan Lampl ; J Neuroscience 2013 (link)

23) Categorical Clustering of the Neural Representation of Color Gijs Joost Brouwer and David J. Heeger ; J Neuroscience 2013 (link)

24) Cytoarchitectonic and Dynamic Origins of Giant Positive Local Field Potentials in the Dentate Gyrus Antonio Fernandez-Ruiz, Sagrario Munoz, Miguel Sancho, Julia Makarova, Valeri A. Makarov, and Oscar Herreras ; J Neuroscience 2013 (link)

25) Two-Dimensional Representation of Action and Arm-Use Sequences in the Presupplementary and Supplementary Motor Areas Toshi Nakajima, Ryosuke Hosaka, Ichiro Tsuda, Jun Tanji, and Hajime Mushiake ; J Neuroscience 2013 (link)

26) Synaptic Mechanisms Underlying Strong Reciprocal Connectivity between the Medial Prefrontal Cortex and Basolateral Amygdala Justin P. Little and Adam G. Carter ; J Neuroscience 2013 (link)

27) Presynaptic Control of Corticostriatal Synapses by Endogenous GABA Christopher Logie, Vincenza Bagetta, and Enrico Bracci ; J Neuroscience 2013 (link)

28) Spatial and Stimulus-Type Tuning in the LEC, MEC, POR, PrC, CA1, and CA3 During Spontaneous Item Recognition Memory Zachery Beer, Caroline Chwiesko, Takashi Kitsukawa, and Magdalena M. Sauvage ; Hippocampus 2013 (link)

Friday Paper List- September 20th

I missed the post last week, so this week’s list is really really long! I recommend you try and at least browse the full list because you don’t want to miss some of the goodies mixed up in the large crowd!

But before we get to the list of papers it is definitely worth mentioning the release of the Interim report for the BRAIN project! You can snag the 58 page pdf here or just read about it here. I can’t help but show two of the lists mentioned:

First “themes have already emerged that should become core principles for the NIH BRAIN Initiative” :

  1.  Use appropriate experimental system and models
  2.  Cross boundaries in interdisciplinary collaborations
  3.  Integrate spatial and temporal scales
  4.  Establish platforms for sharing data
  5.  Validate and disseminate technology
  6.  Consider ethical implications of neuroscience research

and second the “nine research areas are identified as high-priority“:

  1.  Generate a Census of Cell Types.
  2.  Create Structural Maps of the Brain.
  3.  Develop New Large-Scale Network Recording Capabilities.
  4.  Develop A Suite of Tools for Circuit Manipulation.
  5.  Link Neuronal Activity to Behavior.
  6.  Integrate Theory, Modeling, Statistics, and Computation with Experimentation.
  7. Delineate Mechanisms Underlying Human Imaging Technologies.
  8. Create Mechanisms to Enable Collection of Human Data.
  9. Disseminate Knowledge and Training.

It makes quite the laundry list.

As another aside before the main paper list, here are two random papers that caught my attention:

Metabolic rate and body size are linked with perception of temporal information Kevin Healy, Luke McNally, Graeme D. Ruxton, Natalie Cooper, Andrew L. Jackson ; Animal Behaviour 2013 (link)

  • when reading about this paper I couldn’t help but think about that part in Honey I Shrunk the Kids where the character Nick is worried that when they were shrunk they could be experiencing time smaller as well, so what felt like minutes to them was actually days or even years in the normal sized world 😛

Isolation of a Diatom Frustule Fragment From the Lower Stratosphere (22-27Km)-Evidence For a Cosmic Origin Milton Wainwright, Christopher E. Rose, Alexander J. Baker , Briston, K.J  and N. Chandra Wickramasinghe ; Journal of Cosmology 2013 (link)

  • The authors of this paper think their findings give direct evidence for life arriving on earth from outer-space.. no big deal.. just proof that aliens exist… nothing to see here..

Ok, now finally on to the lengthy list of papers:

1) Social reward requires coordinated activity of nucleus accumbens oxytocin and serotonin Gul Dolen, Ayeh Darvishzadeh, Kee Wui Huang & Robert C. Malenka ; Nature 2013i (link)

2) A Cortico-Hippocampal Learning Rule Shapes Inhibitory Microcircuit Activity to Enhance Hippocampal Information Flow Jayeeta Basu, Kalyan V. Srinivas, Stephanie K. Cheung, Hiroki Taniguchi, Z. Josh Huang, and Steven A. Siegelbaum ; Neuron 2013 (link)

3) Inhibitory Gradient along the Dorsoventral Axis in the Medial Entorhinal Cortex Prateep Beed, Anja Gundlfinger, Sophie Schneiderbauer, Jie Song, Claudia Bohm, Andrea Burgalossi, Michael Brecht, Imre Vida, and Dietmar Schmitz ; Neuron 2013 (link)

4) Tet1 Is Critical for Neuronal Activity-Regulated Gene Expression and Memory Extinction Andrii Rudenko, Meelad M. Dawlaty, Jinsoo Seo, Albert W. Cheng, Jia Meng, Thuc Le, Kym F. Faull, Rudolf Jaenisch, and Li-Huei Tsai ; Neuron 2013 (link)

5)  Cellular Resolution Functional Imaging in Behaving Rats Using Voluntary Head Restraint Benjamin B. Scott, Carlos D. Brody, and David W. Tank  ; Neuron 2013 (link)

  • If you get a chance check out the supplementary movie. Pretty amazing watching the whole thing in action.

6) An illusion predicted by V1 population activity implicates cortical topography in shape perception Melchi M Michel, Yuzhi Chen, Wilson S Geisler & Eyal Seidemann ; Nature Neuroscience 2013  (link)

7) The touchscreen operant platform for testing working memory and pattern separation in rats and mice Charlotte A Oomen, Martha Hvoslef-Eide, Christopher J Heath, Adam C Mar, Alexa E Horner, Timothy J Bussey & Lisa M Saksida ; Nature Protocols 2013 (link)

8) The touchscreen operant platform for testing learning and memory in rats and mice Alexa E Horner, Christopher J Heath, Martha Hvoslef-Eide, Brianne A Kent, Chi Hun Kim, Simon R O Nilsson, Johan Alsiö, Charlotte A Oomen, Andrew Holmes, Lisa M Saksida & Timothy J Bussey ; Nature Protocols 2013 (link)

9) The touchscreen operant platform for assessing executive function in rats and mice Adam C Mar, Alexa E Horner, Simon R O Nilsson, Johan Alsiö, Brianne A Kent, Chi Hun Kim, Andrew Holmes, Lisa M Saksida & Timothy J Bussey ; Nature Protocols 2013 (link)

10) From cortical modules to memories David C Rowland and May-Britt Moser ; Current Opinion in Neurobiology 2013 (link)

11) Interplay of Hippocampus and Prefrontal Cortex in Memory Alison R. Preston and Howard Eichenbaum ; Current Biology 2013 (link)

12)  Hippocampal neurogenesis and forgetting Paul W. Frankland, Stefan Kohler, and Sheena A. Josselyn ; Trends in Neuroscience 2013 (link)

13)  Expanding the primate body schema in sensorimotor cortex by virtual touches of an avatar Solaiman Shokur, Joseph E. O’Doherty, Jesse A. Winans, Hannes Bleuler, Mikhail A. Lebedev, and Miguel A. L. Nicolelis ; PNAS 2013 (link)

  • I’m a huge sucker for all of Miguel Nicolelis’s work and this paper is no exception. Pretty amazing!

14) Network structure and dynamics of the mental workspace Alexander Schlegel, Peter J. Kohler, Sergey V. Fogelson, Prescott Alexander, Dedeepya Konuthul, and Peter Ulric Tse ; PNAS 2013 (link)

15) Stress affects theta activity in limbic networks and impairs novelty- induced exploration and familiarization Luis Jacinto, Joana Reis, Nuno Dias, João J Cerqueira, José Higino Correia and Nuno Sousa ; Frontiers in Behavioral Neuroscience 2013 (link)

16) Cortico-cortical communication dynamics Per E Roland, Claus C Hilgetag and Gustavo Deco ; Frontiers in Behavioral Neuroscience 2013 (link)

17) Internal operations in the hippocampus: single cell and ensemble temporal coding George Dragoi ; Frontiers in Systems Neuroscience 2013 (link)

18) Remodeling Sensory Cortical Maps Implants Specific Behavioral Memory K. M. Bieszczad,  A. A. Miasnikov and N. M. Weinberger ; Neuroscience 2013 (link)

19) Extrasynaptic GABAA Receptors Couple Presynaptic Activity to Postsynaptic Inhibition in the Somatosensory Thalamus Murray B. Herd, Adam R. Brown, Jeremy J. Lambert, and Delia Belelli ; J Neuroscience 2013 (link)

20) Transgenically Targeted Rabies Virus Demonstrates a Major Monosynaptic Projection from Hippocampal Area CA2 to Medial Entorhinal Layer II Neurons David C. Rowland, Aldis P. Weible, Ian R. Wickersham, Haiyan Wu, Mark Mayford, Menno P. Witter, and Clifford G. Kentros ; J Neuroscience 2013 (link)

  • This appears to be a pretty impressive finding!

21) Human Cortical Theta during Free Exploration Encodes Space and Predicts Subsequent Memory Joseph Snider, Markus Plank, Gary Lynch, Eric Halgren, and Howard Poizner ; J Neuroscience 2013 (link)

22) Transgene Expression in Target-Defined Neuron Populations Mediated by Retrograde Infection with Adeno-Associated Viral Vectors Markus Rothermel, Daniela Brunert, Christine Zabawa, Marta Díaz-Quesada, and Matt Wachowiak ; J Neuroscience 2013 (link)

23) Synaptic Input Correlations Leading to Membrane Potential Decorrelation of Spontaneous Activity in Cortex Michael Graupner and Alex D. Reyes ; J Neuroscience 2013 (link)

24) Inhibiting Subthalamic D5 Receptor Constitutive Activity Alleviates Abnormal Electrical Activity and Reverses Motor Impairment in a Rat Model of Parkinson’s Disease Jonathan Chetrit, Anne Taupignon, Lionel Froux, Stephanie Morin, Rabia Bouali-Benazzouz, Frederic Naudet, Nabila Kadiri, Christian E. Gross, Bernard Bioulac, and Abdelhamid Benazzouz ; J Neuroscience 2013 (link)

25) Interacting Linear and Nonlinear Characteristics Produce Population Coding Asymmetries between ON and OFF Cells in the Retina Zachary Nichols, Sheila Nirenberg, and Jonathan Victor ; J Neuroscience 2013 (link)

26) Emergence of Sensory Patterns during Sleep Highlights Differential Dynamics of REM and Non-REM Sleep Stages Michal Ramot, Lior Fisch, Ido Davidesco, Michal Harel, Svetlana Kipervasser, Fani Andelman, Miri Y. Neufeld, Uri Kramer, Itzhak Fried, and Rafael Malach ; J Neuroscience 2013 (link)

27) Dynamic Tuning of Electrical and Chemical Synaptic Transmission in a Network of Motion Coding Retinal Neurons Stuart Trenholm, Amanda J. McLaughlin, David J. Schwab, and Gautam B. Awatramani ; J Neuroscience 2013 (link)

28) Repetition Suppression and Multi-Voxel Pattern Similarity Differentially Track Implicit and Explicit Visual Memory Emily J. Ward, Marvin M. Chun, and Brice A. Kuhl ; J Neuroscience 2013 (link)

29) Ontogeny of Excitatory Spinal Neurons Processing Distinct Somatic Sensory Modalities Yi Xu, Claudia Lopes, Hagen Wende, Zhen Guo, Leping Cheng, Carmen Birchmeier, and Qiufu Ma ; J Neuroscience 2013 (link)

30) Subthalamic Nucleus Local Field Potential Activity during the Eriksen Flanker Task Reveals a Novel Role for Theta Phase during Conflict Monitoring Baltazar Zavala, John-Stuart Brittain, Ned Jenkinson, Keyoumars Ashkan, Thomas Foltynie, Patricia Limousin, Ludvic Zrinzo, Alexander L. Green, Tipu Aziz, Kareem Zaghloul, and Peter Brown ; J Neuroscience 2013 (link)

31) Informational Basis of Sensory Adaptation: Entropy and Single-Spike Efficiency in Rat Barrel Cortex Mehdi Adibi, Colin W. G. Clifford, and Ehsan Arabzadeh ; J Neuroscience 2013 (link)

32) Laminar profile of visual response properties in ferret superior colliculus Iain Stitt, Edgar Galindo-Leon, Florian Pieper, Gerhard Engler and Andreas K. Engel ; J Neurophysiology 2013 (link)

33) Directional information from neuronal ensembles in the primate orofacial sensorimotor cortex F. I. Arce, J.-C. Lee, C. F. Ross, B. J. Sessle and N. G. Hatsopoulos ; J Neurophysiology 2013 (link)

and last but not least in this long list for this week….

34) Optogenetics through windows on the brain in the nonhuman primate Octavio Ruiz, Brian R. Lustig, Jonathan J. Nassi, Ali Cetin, John H. Reynolds, Thomas D. Albright, Edward M. Callaway, Gene R. Stoner and Anna W. Roe ; J Neurophysiology 2013 (link)


Friday Paper List – posted Saturday Sept. 7th

Papers papers papers.

I had some links in a past post about some critiques of optogenetics.

Here is a nice article responding to those recent critiques :

“Why optogenetics deserves the hype” by Kevin Mitchell

In other news there was the official announcement for a collaboration towards the development of a new neural probe. It is getting $5.5 million in funds from a partnership between Howard Hughes Medical Institute, Allen Institute for Brain Science, Gatsby Charitable Foundation,  Wellcome Trust, University College London, and Imec. You can read the statement : here.

Speaking of Imec.. reading about the company lead me to reading about this neat little place: NERF

Finally there was an announcement about an Artificial Intelligence version of the Allen Institute for Brain Science. It sounds pretty neat and you can read about it here.

Papers below!

1) ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation John Y Lin, Per Magne Knutsen, Arnaud Muller, David Kleinfeld & Roger Y Tsien ; Nature Neuroscience 2013 (link)

2) Odor Discrimination in Drosophila: From Neural Population Codes to Behavior Moshe Parnas, Andrew C. Lin, Wolf Huetteroth, and Gero Miesenbock ; Neuron 2013 (link)

3) GABAergic Projection Neurons Route Selective Olfactory Inputs to Specific Higher-Order Neurons Liang Liang, Yulong Li, Christopher J. Potter, Ofer Yizhar, Karl Deisseroth, Richard W. Tsien, and Liqun Luo ; Neuron 2013 (link)

4) A Modeling Framework for Deriving the Structural and Functional Architecture of a Short-Term Memory Microcircuit Dimitry Fisher, Itsaso Olasagasti, David W. Tank, Emre R.F. Aksay,, and Mark S. Goldman ; Neuron 2013 (link)

5) Laminar and Columnar Development of Barrel Cortex Relies on Thalamocortical Neurotransmission Hong Li, Sofia Fertuzinhos, Ethan Mohns, Thomas S. Hnasko, Matthijs Verhage, Robert Edwards, Nenad Sestan, and Michael C. Crair ; Neuron 2013 (link)

  • The Many Layers of Specification and Plasticity in the Neocortex Alison L. Barth, and Sandra J. Kuhlman ; Neuron 2013 (link)

6) Theory of Mind: A Neural Prediction Problem Jorie Koster-Hale, and Rebecca Saxe ; Neuron 2013 (link)

7)  Integration of GABAergic Interneurons into Cortical Cell Assemblies: Lessons from Embryos and Adults Giorgia Bartolini, Gabriele Ciceri, and Oscar Marın ; Neuron 2013 (link)

8) Mental time travel: a case for evolutionary continuity Michael C. Corballis ; Trends in Cognitive Sciences 2013 (link)

9) Shining a light on memory representations Lisa M. Saksida ; Trends in Cognitive Sciences 2013 (link)

10) Cortical Balance of Excitation and Inhibition Is Regulated by the Rate of Synaptic Activity Aryeh H. Taub, Yonatan Katz, and Ilan Lampl ; J Neuroscience 2013 (link)

11) A Circuit for Motor Cortical Modulation of Auditory Cortical Activity Anders Nelson, David M. Schneider, Jun Takatoh, Katsuyasu Sakurai, Fan Wang, and Richard Mooney ; J Neuroscience 2013 (link)

12) Distinct Hippocampal Time Cell Sequences Represent Odor Memories in Immobilized Rats Christopher J. MacDonald, Stephen Carrow, Ryan Place, and Howard Eichenbaum  ; J Neuroscience 2013 (link)

13) High-order social interactions in groups of mice Yair Shemesh, Yehezkel Sztainberg, Oren Forkosh, Tamar Shlapobersky, Alon Chen, Elad Schneidman ; eLife 2013 (link)

14) Holographically patterned activation using photo-absorber induced neural–thermal stimulation Nairouz Farah, Alaa Zoubi, Suhail Matar, Lior Golan, Anat Marom, Christopher R Butson, Inbar Brosh and Shy Shoham ; J NeuroEngineering 2013 (link)

15) Refined methodology for implantation of a head fixation device and chronic recording chambers in non-human primates F. Lanza, X. Lanz, A. Scherly, V. Moret, A. Gaillard, P. Gruner, H.-M. Hoogewoud, A. Belhaj-Saif, G. Loquet, E.M. Rouiller ; JNeuroscience Methods 2013 (link)