Friday Paper List – April 26th

Before I start the list, there looks to be an interesting back and forth over some results in the most recent issue of Science.

  • Comment on “In Monkeys Making Value-Based Decisions, LIP Neurons Encode Cue Salience and Not Action Value” William T. Newsome, Paul W. Glimcher, Jacqueline Gottlieb, Daeyeol Lee, Michael L. Platt ; Science 2013 (link)


  • Response to Comment on “In Monkeys Making Value-Based Decisions, LIP Neurons Encode Cue Salience and Not Action Value” Marvin L. Leathers, Carl R. Olson ; Science 2013 (link)

You can find the original paper here. I need to read it and then read these comments. In my opinion there is nothing more fun than a good back-and-forth among well respected scientists!

It’s fun to watch them battle…

Alright on to this weeks list!

1) Optogenetic approaches for functional mouse brain mapping Diana H. Lim, Jeffrey LeDue, Majid H. Mohajerani, Matthieu P. Vanni and Timothy H. Murphy ; Frontiers in Neuroscience 2013 (link)

I am a big fan of the work from Dr. Murphy’s lab. I especially enjoy the amazing things he has done with Voltage Sensitive Dye (VSD) imaging, ChR2, and a bilateral imaging preparation.

You can see spontaneous activity in a control (left) and acallosal (right) mouse brain using VSD imaging of both hemispheres below.

Also if you are ever decide to learn VSD or intrinsic signal imaging I highly recommend this paper:

  • Simple and cost-effective hardware and software for functional brain mapping using intrinsic optical signal imaging Harrison TC, Sigler A, and Murphy TH ; J Neuroscience Methods 2009 (link)

2) Segregation of cortical head direction cell assemblies on alternating theta cycles Mark P Brandon, Andrew R Bogaard, Nathan W Schultheiss & Michael E Hasselmo ; Nature Neuroscience 2013 (link)

This looks very interesting! For those who study the hippocampus, it might be worthwhile to read this paper in tandem with another paper (shown below) from the same group published in 2011. That’s what I’m planning on doing 🙂

  • Reduction of Theta Rhythm Dissociates Grid Cell Spatial Periodicity from Directional Tuning Mark P. Brandon, Andrew R. Bogaard, Christopher P. Libby, Michael A. Connerney, Kishan Gupta, Michael E. Hasselmo ; Science 2011 (link)

3) Neurotransmitter Switching in the Adult Brain Regulates Behavior Davide Dulcis, Pouya Jamshidi, Stefan Leutgeb, Nicholas C. Spitzer ; Science 2013 (link)

Commentary on the above paper:

  • Plasticity in the Neurotransmitter Repertoire Susan J. Birren and Eve Marder ; Science 2013 (link)

4) Adaptation maintains population homeostasis in primary visual cortex Andrea Benucci, Aman B Saleem & Matteo Carandini ; Nature Neuroscience 2013 (link)

5) Attention during natural vision warps semantic representation across the human brain Tolga Çukur, Shinji Nishimoto, Alexander G Huth & Jack L Gallant ; Nature Neuroscience 2013 (link)

6) The dorsomedial striatum encodes net expected return, critical for energizing performance vigor Alice Y Wang, Keiji Miura & Naoshige Uchida ; Nature Neuroscience 2013 (link)

7) The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory Annie Vogel-Ciernia, Dina P Matheos, Ruth M Barrett, Enikö A Kramár, Soraya Azzawi, Yuncai Chen, Christophe N Magnan, Michael Zeller, Angelina Sylvain, Jakob Haettig, Yousheng Jia, Anthony Tran, Richard Dang, Rebecca J Post, Meredith Chabrier, Alex H Babayan, Jiang I Wu, Gerald R Crabtree, Pierre Baldi, Tallie Z Baram, Gary Lynch & Marcelo A Wood ; Nature Neuroscience 2013 (link)

8) Random convergence of olfactory inputs in the Drosophila mushroom body Sophie J. C. Caron, Vanessa Ruta, L. F. Abbott & Richard Axel ; Nature 2013 (link)

9) A Motion Direction Preference Map in Monkey V4 Peichao Li, Shude Zhu, Ming Chen, Chao Han, Haoran Xu, Jiaming Hu, Yang Fang, and Haidong D. Lu ; Neuron 2013 (link)

There is a lot I could say about this paper, but let me just say a few:

It is no coincidence that some of my favorite optical imaging papers are from the lab of Dr. Anna Roe. It is also no coincidence that they often involve the work of Dr. Haidong Lu, Dr. Gang Chen, and Dr. Hisashi Tonegawa. I have a great deal of respect for all four of these scientists. The last three were all postdocs in Anna Roe’s lab at Vanderbilt University. Haidong Lu now has his own lab at the Institute of Neuroscience in Shanghai, China.

This recent paper from Dr. Lu’s lab, in my humble opinion, reflects that he continues to produce some of the best intrinsic signal optical imaging around.

The quality of these images reminds me of two earlier papers from the Roe Lab, involving the same talented people. The 2010 paper, with a very similar title to the one published this week, contains what might be one of my all time favorite figures 🙂


Figure 1 from the paper below.

  • A Motion Direction Map in Macaque V2 Haidong D. Lu, Gang Chen, Hisashi Tanigawa, and Anna W. Roe ; Neuron 2010 (link)
  • A Map for Horizontal Disparity in Monkey V2 Gang Chen, Haidong D. Lu and Anna W. Roe ; Neuron 2008 (link)

10) Population Responses to Contour Integration: Early Encoding of Discrete Elements and Late Perceptual Grouping Ariel Gilad, Elhanan Meirovithz, and Hamutal Slovin ; Neuron 2013 (link)

11) Dynamic Coding for Cognitive Control in Prefrontal Cortex Mark G. Stokes, Makoto Kusunoki, Natasha Sigala, Hamed Nili, David Gaffan, and John Duncan ; Neuron 2013 (link)

12) Associative Learning Enhances Population Coding by Inverting Interneuronal Correlation Patterns James M. Jeanne, Tatyana O. Sharpee, and Timothy Q. Gentner ; Neuron 2013 (link)

Commentary on the above paper:

  • Population Code, Noise Correlations, and Memory Fre ́ de ́ ric E. Theunissen, and Julie E. Elie ; Neuron 2013 (link)

13) Decision Making: From Neuroscience to Psychiatry Daeyeol Lee ; Neuron 2013 (link)

14) Neural Variability in Premotor Cortex Is Modulated by Trial History and Predicts Behavioral Performance Encarni Marcos, Pierpaolo Pani, Emiliano Brunamonti, Gustavo Deco, Stefano Ferraina, and Paul Verschure ; Neuron 2013 (link)

15) Origin of intrinsic irregular firing in cortical interneurons Klaus M. Stiefel, Bernhard Englitz, and Terrence J. Sejnowski ; PNAS 2013 (link)

16) Mapping remodeling of thalamocortical projections in the living reeler mouse brain by diffusion tractography Laura-Adela Harsan, Csaba Dávid, Marco Reisert, Susanne Schnell, Jürgen Hennig, Dominik von Elverfeldt, and Jochen F. Staiger ; PNAS 2013 (link)

The next two papers are in the multi-sensory field, which reminds me:

Congratulations to Dr. Dipanwita Ghose !!! I look forward to posting links to your work in the future 🙂

17) Principles of Multisensory Behavior Thomas U. Otto, Brice Dassy, and Pascal Mamassian ; JNeuroscience 2013 (link)

18) Vision Dominates at the Preresponse Level and Audition Dominates at the Response Level in Cross-modal Interaction: Behavioral and Neural Evidence Qi Chen and Xiaolin Zhou  ; JNeuroscience 2013 (link)

19) Focal Electrical Stimulation of Major Ganglion Cell Types in the Primate Retina for the Design of Visual Prostheses Lauren H. Jepson, Paweł Hottowy, Keith Mathieson, Deborah E. Gunning, Władysław Da ̨browski, Alan M. Litke, and E. J. Chichilnisky ; JNeuroscience 2013 (link)

20) Representation of Abstract Quantitative Rules Applied to Spatial and Numerical Magnitudes in Primate Prefrontal Cortex Anne-Kathrin Eiselt and Andreas Nieder ; JNeuroscience 2013 (link)

21) Selective Silencing of Individual Dendritic Branches by an mGlu2-Activated Potassium Conductance in Dentate Gyrus Granule Cells Ja ́nos Brunner, Jeanne Ster, Susan Van-Weert, Tibor Andra ́si, Ma ́te ́ Neubrandt, Corrado Corti, Mauro Corsi, Francesco Ferraguti, Urs Gerber, and Ja ́nos Szabadics ; JNeuroscience 2013 (link)

22) Functional Connectivity from the Amygdala to the Hippocampus Grows Stronger after Stress Supriya Ghosh, T. Rao Laxmi, and Sumantra Chattarji ; JNeuroscience 2013 (link)

23) Mushroom Body Extrinsic Neurons in the Honeybee Brain Encode Cues and Contexts Differently Syed Abid Hussaini and Randolf Menzel ; JNeuroscience 2013 (link)

24) Signals through the Striatopallidal Indirect Pathway Stop Movements by Phasic Excitation in the Substantia Nigra Hiromi Sano, Satomi Chiken, Takatoshi Hikida, Kazuto Kobayashi, and Atsushi Nambu ; JNeuroscience 2013 (link)

25) Short-term Depression of External Globus Pallidus- Subthalamic Nucleus Synaptic Transmission and Implications for Patterning Subthalamic Activity Jeremy F. Atherton, Ariane Menard, Nadia Urbain, and Mark D. Bevan ; JNeuroscience 2013 (link)

26) Thalamocortical Long-Term Potentiation Becomes Gated after the Early Critical Period in the Auditory Cortex Sungkun Chun, Ildar T. Bayazitov, Jay A. Blundon, and Stanislav S. Zakharenko ; JNeuroscience 2013 (link)

27) Unsupervised Spatiotemporal Analysis of FMRI Data Using Graph-based Visualizations of Self- Organizing Map Santosh B. Katwal, John C. Gore, René Marois and Baxter P. Rogers IEEE 2013 (link)

28) Controlling the oscillation phase through precisely timed closed-loop optogenetic stimulation: a computational study Annette Witt, Agostina Palmigiano, Andreas Neef, Ahmed El Hady, Fred Wolf and Demian Battaglia; Frontiers in Neural Circuits 2013 (link)

29) Effects of repeated tickling on conditioned fear and hormonal responses in socially isolated rats Miyo Hori, Kazuo Yamada, Junji Ohnishi, Shigeko Sakamoto, Eriko Takimoto-Ohnishi, Shigeki Miyabe, Kazuo Murakami, Yukio Ichitani ; Neuro Letters 2013 (link)

What is not to love about this paper. If you haven’t seen this classic video showing the use of ultrasonic bat transducers for hearing rats laugh when they are tickled, then you are in for a treat!

Friday Paper List – April 19th

I might have mentioned I am always reading up on how there are serious problems with the current state of scientific publishing. I found this blog post: Scientific publishing as it was meant to be, which is about a new type of submission for the journal Cortex, really really interesting! I definitely think it is worth a read.

Also I just read this article over at the New York Times website about an interesting development in economics research. I can’t help but wonder what we would find if we re-examined all of the data from pivotal neuroscience publications.

Random links aside, plenty of exciting new papers this week and I’m kind of in a rush to make the post so I’ll just get right to the list of papers. Enjoy!

Quickly making this post as I fly by!

1) Hippocampal place-cell sequences depict future paths to remembered goals Brad E. Pfeiffer & David J. Foster ; Nature 2013 (link)

Commentary on the above paper here:

Navigation with a cognitive map Brandy Schmidt & A. David Redish ; Nature 2013 (link)

2) Representation of Three-Dimensional Space in the Hippocampus of Flying Bats Michael M. Yartsev and Nachum Ulanovsky ; Science 2013 (link)

3) Bat and Rat Neurons Differ in Theta-Frequency Resonance Despite Similar Coding of Space James G. Heys, Katrina M. MacLeod, Cynthia F. Moss, Michael E. Hasselmo; Science 2013 (link)

Commentary on the above two papers here:

3D Mapping in the Brain Caswell Barryand Christian F. Doeller ; Science 2013 (link)

4) Tracking Individuals Shows Spatial Fidelity Is a Key Regulator of Ant Social Organization Danielle P. Mersch, Alessandro Crespi, Laurent Keller ; Science 2013 (link)

There was a really awesome invited talk from Deborah Gordon this year at Cosyne. Ant research looks fascinating!

5)  A Neural Marker of Perceptual Consciousness in Infants Sid Kouider, Carsten Stahlhut, Sofie V. Gelskov, Leonardo S. Barbosa, Michel Dutat, Vincent de Gardelle, Anne Christophe, Stanislas Dehaene, Ghislaine Dehaene-Lambertz ; Science 2013 (link)

6) Visual Scene Perception in Navigating Wood Ants David D. Lent, Paul Graham, and Thomas S. Collett ; Current Biology 2013 (link)

Weird, this is a very different type of any study that happened to catch my eye earlier in the week.

7) The Mechanical Variables Underlying Object Localization along the Axis of the Whisker Lorenz Pammer, Daniel H. O’Connor, S. Andrew Hires, Nathan G. Clack, Daniel Huber, Eugene W. Myers, and Karel Svoboda ; J Neuroscience 2013 (link)

8) Distinct Dendritic Arborization and In Vivo Firing Patterns of Parvalbumin-Expressing Basket Cells in the Hippocampal Area CA3 John J. Tukker, Ba ́lint Laszto ́czi, Linda Katona, J. David B. Roberts, Eleftheria K. Pissadaki, Yannis Dalezios, La ́szlo ́ Ma ́rton, Limei Zhang, Thomas Klausberger, and Peter Somogyi ; J Neuroscience 2013 (link)

9) Cortical-Like Receptive Fields in the Lateral Geniculate Nucleus of Marmoset Monkeys Soon Keen Cheong, Chris Tailby, Samuel G. Solomon, and Paul R. Martin ; J Neuroscience 2013 (link)

10) The Postsubiculum and Spatial Learning: The Role of Postsubicular Synaptic Activity and Synaptic Plasticity in Hippocampal Place Cell, Object, and Object-Location Memory David Bett, Cassie H. Stevenson, Kate L. Shires, Michael T. Smith, Stephen J. Martin, Paul A. Dudchenko, and Emma R. Wood ; J Neuroscience 2013 (link)

11) Auditory Closed-Loop Stimulation of the Sleep Slow Oscillation Enhances Memory Hong-Viet V. Ngo, Thomas Martinetz, Jan Born, and Matthias Mo ̈ lle ; Neuron 2013 (link)

12) Dynamic Coding for Cognitive Control in Prefrontal Cortex Mark G. Stokes, Makoto Kusunoki, Natasha Sigala, Hamed Nili, David Gaffan, and John Duncan ; Neuron 2013 (link)

13) Ambient Illumination Toggles a Neuronal Circuit Switch in the Retina and Visual Perception at Cone Threshold Karl Farrow, Miguel Teixeira, Tamas Szikra, Tim J. Viney, Kamill Balint, Keisuke Yonehara, and Botond Roska ; Neuron 2013 (link)

14) A phase transition in the first passage of a Brownian process through a fluctuating boundary with implications for neural coding Thibaud Taillefumier and Marcelo O. Magnasco ; PNAS 2013 (link)

I am getting a lot of exposure to theoretical neuroscience lately. This paper reminds me of how I feel as I learn more about theory. It’s just amazing how over my head some of this stuff is.

15) Intra-day signal instabilities affect decoding performance in an intracortical neural interface system Ja ́nos A Perge, Mark L Homer, Wasim Q Malik, Sydney Cash, Emad Eskandar, Gerhard Friehs, John P Donoghue and Leigh R Hochberg ; J Neural Engineering 2013 (link)

16)  Acute stress enhances adult rat hippocampal neurogenesis and activation of newborn neurons via secreted astrocytic FGF2 Elizabeth D Kirby, Sandra E Muroy, Wayne G Sun, David Covarrubias, Megan J Leong, Laurel A Barchas, Daniela Kaufer; eLife 2013 (link)

17) A genetic polymorphism affecting reliance on personal versus public information in a spatial learning task in Drosophila melanogaster Julien Foucaud, Anne-Sophie Philippe, Celine Moreno and Frederic Mery ; Proc R Soc B 2013 (link)

18)  Artificial vision with wirelessly powered subretinal electronic implant alpha-IMS Katarina Stingl, Karl Ulrich Bartz-Schmidt, Dorothea Besch, Angelika Braun, Anna Bruckmann, Florian Gekeler, Udo Greppmaier, Stephanie Hipp, Gernot Hörtdörfer, Christoph Kernstock, Assen Koitschev, Akos Kusnyerik, Helmut Sachs, Andreas Schatz, Krunoslav T. Stingl, Tobias Peters, Barbara Wilhelm and Eberhart Zrenner ; Proc R Soc B 2013 (link)

19) Optogenetically Induced Seizure and the Longitudinal Hippocampal Network Dynamics Shin-ichiro Osawa, Masaki Iwasaki, Ryosuke Hosaka, Yoshiya Matsuzaka, Hiroshi Tomita, Toru Ishizuka, Eriko Sugano, Eiichi Okumura, Hiromu Yawo, Nobukazu Nakasato, Teiji Tominaga, Hajime Mushiake; PLoS One 2013 (link)

Friday Paper List – April 11th

One theme of this blog is that it can be very overwhelming trying to keep up with all of the latest research being published. Today’s post is a fine example as there are 34 papers on the list!

It’s almost enough to make you dizzy.

1) Mental time travel: continuities and discontinuities Thomas Suddendorf ; Trends in Cognitive Science 2013 (link)

2) The wandering rat: response to Suddendorf Michael C. Corballis ; Trends in Cognitive Science 2013 (link)

I really like these first two papers. They are not full ‘papers’ really, but rather short commentaries on a debate.

3) Structural and molecular interrogation of intact biological systems Kwanghun Chung, Jenelle Wallace, Sung-Yon Kim, Sandhiya Kalyanasundaram, Aaron S. Andalman, Thomas J. Davidson, Julie J. Mirzabekov, Kelly A. Zalocusky, Joanna Mattis, Aleksandra K. Denisin, Sally Pak, Hannah Bernstein, Charu Ramakrishnan, Logan Grosenick, Viviana Gradinaru & Karl Deisseroth ; Nature 2013 (link)

Commentary on the above paper here:

See-through brains clarify connections Helen Shen ; Nature 2013 (link)

Of course you can read my impressions about this exciting paper from my last post.

4) Rats and Humans Can Optimally Accumulate Evidence for Decision-Making Bingni W. Brunton,  Matthew M. Botvinick,  Carlos D. Brody ; Science 2013 (link)

Commentary for the above paper:

Sensory noise drives bad decisions Matthew T. Kaufman & Anne K. Churchland; Nature 2013 (link)

5) Injectable, Cellular-Scale Optoelectronics with Applications for Wireless Optogenetics Tae-il Kim, Jordan G. McCall, Yei Hwan Jung, Xian Huang,Edward R. Siuda,Yuhang Li,Jizhou Song,Young Min Song,Hsuan An Pao,Rak-Hwan Kim,Chaofeng Lu,Sung Dan Lee, Il-Sun Song, Gunchul Shin,Ream Al-Hasani,Stanley Kim,Meng Peun Tan, Yonggang Huang,Fiorenzo G. Omenetto, John A. Rogers, Michael R. Bruchas ; Science 2013 (link)

Um yes please…

The toys *cough* I mean tools that are coming out for neuroscientists nowadays are just awesome.

6) Corticostriatal connectivity and its role in disease Gordon M. G. Shepherd ; Nature Reviews Neuroscience 2013 (link)

On a slightly related note (and I’m sure it’s not the first time Dr. Shepherd Jr. has had to deal with being a segway to the work of Dr. Shepherd Sr.) if you are looking for a good book recommendation (as if you don’t already have enough papers to read) check out

Creating Modern Neuroscience: The Revolutionary 1950s by Gordon M. Shepherd (link)

It is a really fantastic book.

7) Brain networks underlying episodic memory retrieval Michael D Rugg and Kaia L Vilberg ; Current Opinion in Neurobiology 2013 (link)

8) Synaptic Computation and Sensory Processing in Neocortical Layer 2/3 Carl C.H. Petersen and Sylvain Crochet ; Neuron 2013 (link)

9) Imaging Patients with Psychosis and a Mouse Model Establishes a Spreading Pattern of Hippocampal Dysfunction and Implicates Glutamate as a Driver Scott A. Schobel, Nashid H. Chaudhury, Usman A. Khan, Beatriz Paniagua, Martin A. Styner, Iris Asllani, Benjamin P. Inbar, Cheryl M. Corcoran, Jeffrey A. Lieberman, Holly Moore, and Scott A. Small, ; Neuron 2013 (link)

10) Closing the Gate in the Limbic Striatum: Prefrontal Suppression of Hippocampal and Thalamic Inputs Gwendolyn G. Calhoon and Patricio O’Donnell  ; Neuron 2013 (link)

11) Dynamic Reconfiguration of Hippocampal Interneuron Circuits during Spatial Learning David Dupret, Joseph O’Neill, and Jozsef Csicsvari ; Neuron 2013 (link)

12) Circuits for Grasping: Spinal dI3 Interneurons Mediate Cutaneous Control of Motor Behavior Tuan V. Bui, Turgay Akay, Osama Loubani, Thomas S. Hnasko, Thomas M. Jessell, and Robert M. Brownstone ; Neuron 2013 (link)

13) Pre-neuronal morphological processing of object location by individual whiskers Knarik Bagdasarian, Marcin Szwed, Per Magne Knutsen, Dudi Deutsch, Dori Derdikman, Maciej Pietr Erez Simony & Ehud Ahissar ; Nature Neuroscience 2013 (link)

14) Regulation of Spatial Selectivity by Crossover Inhibition Jon Cafaro and Fred Rieke ; J Neuroscience 2013 (link)

15) Cortical Connectivity Suggests a Role in Limb Coordination for Macaque Area PE of the Superior Parietal Cortex Sophia Bakola, Lauretta Passarelli, Michela Gamberini, Patrizia Fattori, and Claudio Galletti ; J Neuroscience 2013 (link)

16)  Functional Disconnection of the Orbitofrontal Cortex and Basolateral Amygdala Impairs Acquisition of a Rat Gambling Task and Disrupts Animals’ Ability to Alter Decision-Making Behavior after Reinforcer Devaluation Fiona D. Zeeb and Catharine A. Winstanley ; J Neuroscience 2013 (link)

17) Improving brain–machine interface performance by decoding intended future movements Francis R Willett, Aaron J Suminski, Andrew H Fagg and Nicholas G Hatsopoulos ; J Neuroengineering 2013 (link)

18) Animal Communication: Sniffing Is About More Than Just Smell Bennett G. Galef ; Current Biology 2013 (link)

This is a commentary on a paper that was posted a while back (paper #5 on the March 8th post).

19) A Sensitive Period for GABAergic Interneurons in the Dentate Gyrus in Modulating Sensorimotor Gating Nannan Guo, Kaichi Yoshizaki, Ryuichi Kimura, Fumikazu Suto, Yuchio Yanagawa, and Noriko Osumi ; J Neuroscience 2013 (link)

20) The Role of Delayed Suppression in Slow and Fast Contrast Adaptation in V1 Simple Cells Manuel Levy, Julien Fournier, and Yves Fre ́gnac ; J Neuroscience 2013 (link)

21) Intensity Invariant Dynamics and Odor-Specific Latencies in Olfactory Receptor Neuron Response Carlotta Martelli, John R. Carlson, and Thierry Emonet ; J Neuroscience 2013 (link)

22) Matched Pre- and Post-Synaptic Changes Underlie Synaptic Plasticity over Long Time Scales Alex Loebel, Jean-Vincent Le Be ́, Magnus J. E. Richardson, Henry Markram, and Andreas V. M. Herz ; J Neuroscience 2013 (link)

23) Deep Brain Stimulation Reduces Tic-Related Neural Activity via Temporal Locking with Stimulus Pulses Kevin W. McCairn, Atsushi Iriki, and Masaki Isoda ; J Neuroscience 2013 (link)

24) Loss of Histone Deacetylase 2 Improves Working Memory and Accelerates Extinction Learning Michael J. Morris, Melissa Mahgoub, Elisa S. Na, Heena Pranav, and Lisa M. Monteggia ; J Neuroscience 2013 (link)

25) The Role of Memory Reactivation during Wakefulness and Sleep in Determining Which Memories Endure Delphine Oudiette, James W. Antony, Jessica D. Creery, and Ken A. Paller ; J Neuroscience 2013 (link)

26) Distributed Patterns of Activity in Sensory Cortex Reflect the Precision of Multiple Items Maintained in Visual Short-Term Memory Stephen M. Emrich, Adam C. Riggall, Joshua J. LaRocque, and Bradley R. Postle ; J Neuroscience 2013 (link)

27) Immature Doublecortin-Positive Hippocampal Neurons Are Important for Learning But Not for Remembering Jana Vukovic, Gilyana G. Borlikova, Marc J. Ruitenberg, Gregory J. Robinson, Robert K.P. Sullivan, Tara L. Walker, and Perry F. Bartlett ; J Neuroscience 2013 (link)

28) Hierarchical Organization of Parietofrontal Circuits during Goal-Directed Action Lennart Verhagen, H. Chris Dijkerman, W. Pieter Medendorp, and Ivan Toni ; J Neuroscience 2013 (link)

29) Mapping Brain Metabolic Connectivity in Awake Rats with μPET and Optogenetic Stimulation Panayotis K. Thanos, Lisa Robison, Eric J. Nestler, Ronald Kim, Michael Michaelides, Mary-Kay Lobo, and Nora D. Volkow ; J Neuroscience 2013 (link)

30) Functional Role of the Cerebellum in Gamma-Band Synchronization of the Sensory and Motor Cortices Daniela Popa, Maria Spolidoro, Re ́mi D. Proville, Nicolas Guyon, Lucile Belliveau, and Cle ́ment Le ́na ; J Neuroscience 2013 (link)

31) Spiking Neurons in a Hierarchical Self-Organizing Map Model Can Learn to Develop Spatial and Temporal Properties of Entorhinal Grid Cells and Hippocampal Place Cells Praveen K. Pilly1, Stephen Grossberg ; PLoS One 2013 (link)

32) A jump-start for electroceuticals Kristoffer Famm, Brian Litt, Kevin J. Tracey, Edward S. Boyden, Moncef Slaoui.; Nature 2013 (link)

This is a very interesting commentary that I only stumbled upon because it was linked from Ed Boyden’s twitter account.

33) The appearance of new phantom fingers post- amputation in a phocomelus Paul D. McGeoch a & V. S. Ramachandran ; Neurocase: The Neural Basis of Cognition 2012 (link)

This is not really a “new” paper but I stumbled upon it from a friend’s post on facebook and it is really interesting!

34) The First Level of Super Mario Bros. is Easy with Lexicographic Orderings and Time Travel . . . after that it gets a little tricky. Tom Murphy VII ; (link)

This is not published in a peer-reviewed journal, but I thought it was really awesome. You can of course watch a video here, if you don’t want to read the paper. But the paper is really entertaining and has my favorite lines out of all the papers I read this week:

“8 bits is really small. You can see them all right here: 00001111.”

CLARITY finally published!

If you were at SFN last year, you might have managed to catch a glimpse of this poster buried inside a large crowd of neuroscientists. I didn’t even attempt to see the poster up close; instead I gathered what I could from those who escaped to the fringe of the mob after seeing the poster and video demonstration playing on an ipad. Those who I spoke to where wide-eyed and giddy. They told me tales of a magical method that could turn brains invisible..

Of course making tissue transparent for subsequent optical investigation is nothing new, but then that wasn’t the whole story! Supposedly with this magical technique you could subsequently perform whole brain immuno-staining.. and not just that.. you could do it multiple times!!

Ok, so on the surface this sounds pretty cool… but then you see the videos like the one from Nature’s video channel here and you start to realize this is pretty amazing…

…then you read more about the method itself (from a commentary here and the actual publication here) and you start to really comprehend how useful this technique could be for understanding projections in the whole brain…

…and then you read that this can be applied to not just a mouse brain, but ANY brain… so you can do this to a brain from a rat, zebrafish, non-human primate … really any model organisms being used for neuroscience research! Of course you can forget using a model system and just use actual human tissue…the paper even shows an interesting finding using some human cortex from an autistic patient that had been stored in formalin for over 6 years!! …

… and then finally it makes sense why most of the neuroanatomists at SFN where walking away from the CLARITY poster looking like this…

I should add, this exciting new technique was developed in the lab of Karl Deisseroth, who you might recognize as one of the developers of optogenetics. I think it’s safe to say that he is feeling pretty good right about now.

Dr. Deisseroth this morning when the CLARITY paper was officially published.

I’ll end this overload of animated GIFs with a link to just one of several articles that are popping up all over the internet. This one had a link to a video of Dr. Deisseroth himself describing the process in an interview. You can check that out here as well.


Friday Paper List – posted Sunday April 7th

As expected on Tuesday this last week President Obama made an official statement about the BAM initiative which has now been changed to BRAIN. What followed was an explosion in media coverage, blog posts, NPR interviews, and Tweets on the subject. Here are just a few.

Here is a link for a general overview of what’s going on from the NIH website.

This page on the website seems to have links to all the different announcements.

There is a blurb here from the Nature News Blog.

I really like this blog post from Gary Marcus for the New Yorker.

Here is a blog post from someone who thinks the BRAIN initiative is a bad idea and “a missed opportunity”.

Here is a nice short blog post that gives some possible perspective on the amount of funding.

The post above lead me to this nice post from a Wired interview with Bill Newsome.

Two friends shared with me some links for NPR interviews on the subject: here and here. Thanks Michele and Omar!

And finally you couldn’t top off the media coverage any better than with the head of the NIH, Francis Collins, appearing on the Colbert Report! You can see Stephen Colbert give his thoughts on the BRAIN project and how it isn’t right to have the first letter of an acronym stand for the acronym here. And then for then check out the interview here.

In other news, research at the University of California Santa Cruz on finding out if other animals have the rhythmic ability to follow a beat like humans, has led to what might be the best video of the year.

Check out the video here. I promise you won’t be disappointed. Go straight to about 0:24 seconds in for the best part!

On to the papers!

1) Multifeatural Shape Processing in Rats Engaged in Invariant Visual Object Recognition Alireza Alemi-Neissi, Federica Bianca Rosselli, and Davide Zoccolan ; J Neuroscience 2013 (link)

After his bold attack on the rodent visual system at COSYNE this year, I couldn’t help but read the title for the paper above and see Tony Movshon, teary-eyed, holding a stuffed monkey-toy under one arm while the other shakes a fist in the air 🙂

2) Entorhinal Stellate Cells Show Preferred Spike Phase-Locking to Theta Inputs That Is Enhanced by Correlations in Synaptic Activity Fernando R. Fernandez, Paola Malerba, Paul C. Bressloff, and John A. White ; J Neuroscience 2013 (link)

3) Dissociation between Dorsal and Ventral Hippocampal Theta Oscillations during Decision-Making Brandy Schmidt, James R. Hinman, Tara K. Jacobson, Emily Szkudlarek, Melissa Argraves, Monty A. Escabí, and Etan J. Markus; J Neuroscience 2013 (link)

4) Abstract Representations of Location and Facing Direction in the Human Brain Lindsay K. Vass and Russell A. Epstein ; J Neuroscience 2013 (link)

5) Toward High Performance, Weakly Invasive Brain Computer Interfaces Using Selective Visual Attention David Rotermund, Udo A. Ernst, Sunita Mandon, Katja Taylor, Yulia Smiyukha, Andreas K. Kreiter, and Klaus R. Pawelzik ; J Neuroscience 2013 (link)

6) Functional Characterization of the Extraclassical Receptive Field in Macaque V1: Contrast, Orientation, and Temporal Dynamics Christopher A. Henry, Siddhartha Joshi, Dajun Xing, Robert M. Shapley, and Michael J. Hawken ; J Neuroscience 2013 (link)

7) Time-lapse electrical recordings of single neurons from the mouse neocortex Lior Cohen, Noa Koffman, Hanoch Meiri, Yosef Yarom, Ilan Lampl, and Adi Mizrahi ; PNAS 2013 (link)

8) Motor Cortex Broadly Engages Excitatory and Inhibitory Neurons in Somatosensory Barrel Cortex Amanda K. Kinnischtzke, Daniel J. Simons and Erika E. Fanselow ; Cerebral Cortex 2013 (link)

9) Extracellular Sheets and Tunnels Modulate Glutamate Diffusion in Hippocampal Neuropil Justin P. Kinney, Josef Spacek, Thomas M. Bartol, Chandrajit L. Bajaj, Kristen M. Harris, and Terrence J. Sejnowski ; Journal of Comparative Neurology 2013 (link)

10) Rescuing cocaine-induced prefrontal cortex hypoactivity prevents compulsive cocaine seeking Billy T. Chen, Hau-Jie Yau, Christina Hatch, Ikue Kusumoto-Yoshida, Saemi L. Cho, F. Woodward Hopf & Antonello Bonci ; Nature 2013 (link)

11) The emergence of functional microcircuits in visual cortex Ho Ko, Lee Cossell, Chiara Baragli, Jan Antolik, Claudia Clopath, Sonja B. Hofer & Thomas D. Mrsic-Flogel ; Nature 2013 (link)

12) Neural Decoding of Visual Imagery During Sleep T. Horikawa,1,2 M. Tamaki, Y. Miyawaki, Y. Kamitani ; Science 2013 (link)

Commentary on the paper above:

How to Build a Dream-Reading Machine Emily Underwood ; Science 2013 (link)

13) Non-Invasive Brain-to-Brain Interface (BBI): Establishing Functional Links between Two Brains Seung-Schik Yoo, Hyungmin Kim, Emmanuel Filandrianos, Seyed Javid Taghados, Shinsuk Park ; PLoS One 2013 (link)

This looks interesting. Clearly considering this paper along with the earlier Nicolelis publication hints at an upcoming explosion of Brain-to-Brain interface studies… or maybe not.

14) Optogenetic Dissection of Entorhinal-Hippocampal Functional Connectivity Sheng-Jia Zhang, Jing Ye, Chenglin Miao, Albert Tsao, Ignas Cerniauskas, Debora Ledergerber, May-Britt Moser, Edvard I. Moser ; Science 2013 (link)

Commentary on the above paper:

A Trace of Your Place Bruno Poucet and Francesca Sargolini ; Science 2013 (link)

I’m very excited to read this last paper!