Friday Paper Post – Sunday November 24th 2013 – still catching up

Still playing catch up after SFN! Hopefully I’ll be back on track before the end of the year.

Tons of good papers to chew on below!

1) Cortical connectivity and sensory coding Kenneth D. Harris & Thomas D. Mrsic-Flogel ; Nature 2013 (link)

This is a great overview! The two boxes summarizing what we know about excitatory and inhibitory cortical cells types and circuits are so valuable that I couldn’t resist posting them below!






2) Context-dependent computation by recurrent dynamics in prefrontal cortex Valerio Mante, David Sussillo, Krishna V. Shenoy & William T. Newsome ; Nature 2013 (link)

  • What to do and how Jeffrey C. Erlich and Carlos D. Brody ; Nature 2013 (link)

3) A Brain-Machine Interface Enables Bimanual Arm Movements in Monkeys Peter J. Ifft,, Solaiman Shokur, Zheng Li, Mikhail A. Lebedev, Miguel A. L. Nicolelis ; Science Translational Medicine 2013 (link)

There was a special neuroscience focused section in Nature right around SFN that was full of some really great articles. They are linked below.

4) New Angles on the Brain  Nature 2013 (link)

  • Head Start Editorial ; Nature 2013 (link)
  • Smart Connections M. Mitchell Waldrop ; Nature 2013 (link)
  • Brain Storm Helen Shen  ; Nature 2013 (link)
  • Neurobiology : Brain Mapping in High Resolution Nature 2013 (link)
  • My life with Parkinson’s @Parklifensci ; Nature 2013 (link)

5) The activity-dependent transcription factor NPAS4 regulates domain-specific inhibition Brenda L. Bloodgood, Nikhil Sharma, Heidi Adlman Browne, Alissa Z. Trepman & Michael E. Greenberg ; Nature 2013 (link)

6) Precision gene editing paves way for transgenic monkeys Helen Shen ; Nature 2013 (link)

6) Low-Intensity Focused Ultrasound Modulates Monkey Visuomotor Behavior Thomas Deffieux, Youliana Younan, Nicolas Wattiez, Mickael Tanter, Pierre Pouget ; Current Biology 2013 (link)

7) Spatiotemporal Structure of REM Sleep Twitching Reveals Developmental Origins of Motor Synergies Mark S. Blumberg, Cassandra M. Coleman, Ashlynn I. Gerth, and Bob McMurray ; Current Biology 2013 (link)

8) Distinct Roles of the Cortical Layers of Area V1 in Figure-Ground Segregation Matthew W. Self, Timo van Kerkoerle, Hans Supe`r, and Pieter R. Roelfsema ; Current Biology 2013 (link)

9) Causal Role of Prefrontal Cortex in Strengthening of Episodic Memories through Reconsolidation Marco Sandrini, Nitzan Censor, Jonathan Mishoe, and Leonardo G. Cohen ; Current Biology 2013 (link)

10) A spatiotemporal coding mechanism for background- invariant odor recognition Debajit Saha, Kevin Leong, Chao Li, Steven Peterson, Gregory Siegel & Baranidharan Raman ; Nature Neuroscience 2013 (link)

11) Spike-Timing-Dependent Plasticity in Primate Corticospinal Connections Induced during Free Behavior Yukio Nishimura, Steve I. Perlmutter, Ryan W. Eaton, and Eberhard E. Fetz  ; Neuron 2013 (link)

  • If you aren’t familiar with work from Fetz I highly recommend checking out this classic paper:
  • Long-term motor cortex plasticity induced by an electronic neural implant Andrew Jackson, Jaideep Mavoori & Eberhard E. Fetz ; Nature 2006 (link)

12) Fabrication and application of flexible, multimodal light-emitting devices for wireless optogenetics Jordan G McCall, Tae-il Kim, Gunchul Shin, Xian Huang, Yei Hwan Jung, Ream Al-Hasani, Fiorenzo G Omenetto, Michael R Bruchas & John A Rogers ; Nature Protocols 2013  (link)

  • These awesome tools were published in Science earlier in the year (see it here). Very cool that they have now published the recipe for making them!

13) Cingulate-Hippocampus Coherence and Trajectory Coding in a Sequential Choice Task Miguel Remondes and Matthew A. Wilson ; Neuron 2013 (link)

The next three papers all come from the special Neuron 25th anniversary issue:

14) Scaling Brain Size, Keeping Timing: Evolutionary Preservation of Brain Rhythms Gyorgy Buzsaki, Nikos Logothetis, and Wolf Singer ; Neuron 2013 (link)

15) Grid Cells and Neural Coding in High-End Cortices Edvard I. Moser and May-Britt Moser ; Neuron 2013 (link)

16) Activity-Dependent Neural Plasticity from Bench to Bedside Karunesh Ganguly and Mu-ming Poo ; Neuron 2013 (link)

17) High-speed laser microsurgery of alert fruit flies for fluorescence imaging of neural activity Supriyo Sinha, Liang Liang, Eric T. W. Ho, Karel E. Urbanek, Liqun Luo, Thomas M. Baer, and Mark J. Schnitzer ; PNAS 2013 (link)

18) The Synchronous Activity of Lateral Habenular Neurons Is Essential for Regulating Hippocampal Theta Oscillation Hidenori Aizawa, Shin Yanagihara, Megumi Kobayashi, Kazue Niisato, Takashi Takekawa, Rie Harukuni, Thomas J. McHugh, Tomoki Fukai, Yoshikazu Isomura, and Hitoshi Okamoto ; J Neuroscience 2013 (link)

19) Ventromedial Prefrontal Cortex Pyramidal Cells Have a Temporal Dynamic Role in Recall and Extinction of Cocaine-Associated Memory Michel C. Van den Oever, Diana C. Rotaru, Jasper A. Heinsbroek, Yvonne Gouwenberg, Karl Deisseroth, Garret D. Stuber, Huibert D. Mansvelder, and August B. Smit ; J Neuroscience 2013 (link)

20) Neural Codes Formed by Small and Temporally Precise Populations in Auditory Cortex Robin A. A. Ince, Stefano Panzeri, and Christoph Kayser; J Neuroscience 2013 (link)


Friday Paper Post – Saturday November 16th 2013

I have definitely gone into a tailspin as far as updates go.

The combination of experiments, SFN, and some other things have made me fall behind; but don’t worry too much because I have plenty of great papers to catch up with!

Instead of making one giant post, I’ll try to make a catch up post sometime before Friday.


1) Dendritic spikes enhance stimulus selectivity in cortical neurons in vivo Spencer L. Smith, Ikuko T. Smith, Tiago Branco & Michael Hausser ; Nature 2013 (link)

  • This is a pretty exciting paper!

2) Voltage-Gated Sodium Channel in Grasshopper Mice Defends Against Bark Scorpion Toxin Ashlee H. Rowe, Yucheng Xiao, Matthew P. Rowe, Theodore R. Cummins, Harold H. Zakon ; Science 2013 (link)

There where a whole bunch of special neuroscience related special issues in different journals over the last few weeks. One of them was a special issue of Science and the papers below have some of these special issue reviews and editorial commentaries.

3) Cortical High-Density Counterstream Architectures Nikola T. Markov, Mária Ercsey-Ravasz, David C. Van Essen, Kenneth Knoblauch, Zoltán Toroczkai, Henry Kennedy ; Science 2013 (link)

4) Structural and Functional Brain Networks: From Connections to Cognition Hae-Jeong Park and Karl Friston ; Science 2013 (link)

5) Functional Interactions as Big Data in the Human Brain Nicholas B. Turk-Browne ; Science 2013 (link)

6) Predispositions and Plasticity in Music and Speech Learning: Neural Correlates and Implications Robert J. Zatorre ; Science 2013 (link)

7) Seize the Neuroscience Moment Alan I. Leshner ; Science 2013 (link)

Short-Circuiting Depression Emily Underwood ; Science 2013 (link)

Connection, Connection, Connection. Peter Stern ; Science 2013 (link)

8) Play It Again Brain Daniel Bendor ; Science 2013 (link)

9) A spatiotemporal coding mechanism for background- invariant odor recognition Debajit Saha, Kevin Leong, Chao Li, Steven Peterson, Gregory Siegel & Baranidharan Raman ; Nature Neuroscience 2013 (link)

10) Temporal synchrony and gamma-to-theta power conversion in the dendrites of CA1 pyramidal neurons Sachin P Vaidya & Daniel Johnston ; Nature Neuroscience 2013 (link)

11) Integration of visual motion and locomotion in mouse visual cortex Aman B Saleem, Aslı Ayaz, Kathryn J Jeffery, Kenneth D Harris & Matteo Carandini ; Nature Neuroscience 2013 (link)

12) Regulation of interneuron excitability by gap junction coupling with principal cells Pierre F Apostolides & Laurence O Trussell ; Nature Neuroscience 2013 (link)

13) Engineering Approaches to Illuminating Brain Structure and Dynamics Karl Deisseroth and Mark J. Schnitzer ; Neuron 2013 (link)

14) Optical control of neuronal excitation and inhibition using a single opsin protein, ChR2 Holly Liske, Xiang Qian, Polina Anikeeva, Karl Deisseroth & Scott Delp ; Scientific Reports 2013 (link)

15) Points of Significance: Significance, P values and t-tests Martin Krzywinski & Naomi Altman ; Nature Methods 2013 (link)

16) The development of the hippocampal neural representation of space Thomas J Wills and Francesca Cacucci ; Current Opinion in Neurobiology 2013 (link)

17) Seeing Left- or Right-Asymmetric Tail Wagging Produces Different Emotional Responses in Dogs Marcello Siniscalchi, Rita Lusito, Giorgio Vallortigara, and Angelo Quaranta ; Current Biology 2013 (link)

  • this is fun!

18) Short Duration Waveforms Recorded Extracellularly from Freely Moving Rats Are Representative of Axonal Activity Ashlee A Robbins, Steven E Fox, Gregory L Holmes, Rodney C Scott and Jeremy Michael Barry ; Frontiers in Neural Circuits 2013 (link)

19) Dopaminergic transmission in the midbrain ventral tegmental area in the induction of hippocampal theta rhythm Jolanta Orzeł-Gryglewska, Magda Kus ́mierczak, Paweł Matulewicz, Edyta Jurkowlanie ; Brain Research 2013 (link)

20) A low-cost multichannel wireless neural stimulation system for freely roaming animals Monzurul Alam, Xi Chen and Eduardo Fernandez ; J NeuroEngineering 2013 (link)

21) System identification of the nonlinear dynamics in the thalamocortical circuit in response to patterned thalamic microstimulation in vivo Daniel C Millard, Qi Wang, Clare A Gollnick and Garrett B Stanley ; J NeuroEngineering 2013 (link)

22) A unified framework and method for automatic neural spike identification Chaitanya Ekanadham, Daniel Tranchin, Eero P. Simoncelli ; J Neuroscience Methods 2013 (link)

23) Distinct Balance of Excitation and Inhibition in an Interareal Feedforward and Feedback Circuit of Mouse Visual Cortex Weiguo Yang, Yarimar Carrasquillo, Bryan M. Hooks, Jeanne M. Nerbonne, and Andreas Burkhalter ; J Neuroscience 2013 (link)

24) Modality-Based Organization of Ascending Somatosensory Axons in the Direct Dorsal Column Pathway Jingwen Niu, Long Ding, Jian J. Li, Hyukmin Kim, Jiakun Liu, Haipeng Li, Andrew Moberly, Tudor C. Badea, Ian D. Duncan, Young-Jin Son, Steven S. Scherer, and Wenqin Luo ; J Neuroscience 2013 (link)

25) Ca2 Sparks and Puffs Are Generated and Interact in Rat Hippocampal CA1 Pyramidal Neuron Dendrites Kenichi Miyazaki and William N. Ross ; J Neuroscience 2013 (link)

26) Perceptual Spaces: Mathematical Structures to Neural Mechanisms Qasim Zaidi, Jonathan Victor, Josh McDermott, Maria Geffen, Sliman Bensmaia, and Thomas A. Cleland ; J Neuroscience 2013 (link)

27) Imaging Neuronal Populations in Behaving Rodents: Paradigms for Studying Neural Circuits Underlying Behavior in the Mammalian Cortex Jerry L. Chen, Mark L. Andermann, Tara Keck, Ning-Long Xu, and Yaniv Ziv ; J Neuroscience 2013 (link)