Friday Paper List February 15th

1. Perceiving invisible light through a somatosensory cortical prosthesis Eric E. Thomson, Rafael Carra,w & Miguel A.L. Nicolelis ; Nature Communications 2013 (link)

I was lucky enough to see Eric Thomson present this work at the Barrels meeting before SFN last year and I thought it was great! I have to admit I am a big fan Miguel Nicolelis and I really enjoyed his book Beyond Boundaries (I recommend checking it out).

My favorite part of Eric’s presentation was of course the movies he showed. Although it is a minor detail I loved how the frequency of the electrical stimulation (which is proportional to the intensity of the infrared light) is presented in the movies as tones with increasing frequency. It’s really neat hearing what the rat is “feeling” as it zones in on the location of the reward.

Definitely check out the supplementary movies posted on this news article here.

2. Membrane potential dynamics of grid cells Cristina Domnisoru, Amina A. Kinkhabwala & David W. Tank ; Nature 2013 (link)

3. Cellular mechanisms of spatial navigation in the medial entorhinal cortex Christoph Schmidt-Hieber & Michael Häusser ; Nature Neuroscience 2013 (link)

I am eager to read the two papers listed above this weekend because at first glance they seem to be reporting on the same thing. I always enjoy the opportunity to compare results in papers!

4. Long-term dynamics of CA1 hippocampal place codes Yaniv Ziv , Laurie D Burns , Eric D Cocker , Elizabeth O Hamel, Kunal K Ghosh, Lacey J Kitch, Abbas El Gamal & Mark J Schnitzer ; Nature Neuroscience 2013 (link)

At first glance I was really excited about this paper. While I have to admit I was a little let down by some of the things this paper is lacking, it is just a “brief communication” so  I’ll just have to wait for the next big report on what they find using this exciting method.

Also my advisor suggested I read this Kentros et al. 2004 Neuron paper which reported on the same question. I thought this was a great paper and was very grateful for the recommendation!

5. Terminal effects of optogenetic stimulation on dopamine dynamics in rat striatum Caroline E. Bass, Valentina P. Grinevich, Alexandra D. Kulikova, Keith D Bonin, Evgeny A. Budygin ; Journal of Neuroscience Methods 2013 (link)

6. Feature Extraction using First and Second Derivative Extrema (FSDE), for Real-time and Hardware-Efficient Spike Sorting Sivylla E. Paraskevopoulou, Deren Y. Barsakcioglu, Mohammed R. Saberi, Amir Eftekhar, Timothy G. Constandinou ; Journal of Neuroscience Methods 2013 (link)

7. Synaptic Cooperativity Regulates Persistent Network Activity in Neocortex Morgana Favero and Manuel A. Castro-Alamancos ; Journal of Neuroscience 2013 (link)

8. Tracking the Course of Hippocampal Representations during Learning: When Is the Map Required? Lesley A. Schimanski, Peter Lipa, and Carol A. Barnes ; Journal of Neuroscience 2013 (link)

9. Source Memory in the Rat Jonathon D. Crystal, Wesley T. Alford, Wenyi Zhou, and Andrea G. Hohmann ; Current Biology 2013 (link)

10. Medial Entorhinal Grid Cells and Head Direction Cells Rotate with a T-Maze More Often During Less Recently Experienced Rotations Kishan Gupta, Nathan J. Beer, Lauren A. Keller and Michael E. Hasselmo ; Cerebral Cortex 2013 (link)

6 out of the 10 papers for this week are hippocampus related. Of course this is mostly a reflection of where my interests are, but I also think this was just a weird coincidence i.e. it was a slow week in other areas.


Friday Paper List February 8th

Ok, looks like I am a little late again… presenting another Friday Paper List posted on a Saturday!

1. Optogenetic protein clustering and signaling activation in mammalian cells Lukasz J Bugaj, Atri T Choksi, Colin K Mesuda, Ravi S Kane & David V Schaffer ; Nature Methods 2013 (link)

Is there anything we can’t play with using optogenetics?!

2. Receptive-Field Subfields of V2 Neurons in Macaque Monkeys Are Adult-Like Near Birth Bin Zhang, Xiaofeng Tao, Guofu Shen, Earl L. Smith III, Izumi Ohzawa, and Yuzo M. Chino ; J Neuroscience 2013 (link)

3. Hierarchical organization of context in the hippocampal episodic code Susumu Takahashi ; eLIFE 2013 (link)

4. Loss of Dickkopf-1 Restores Neurogenesis in Old Age and Counteracts Cognitive Decline De ́ sire ́ e R.M. Seib, Nina S. Corsini, Kristina Ellwanger, Christian Plaas, Alvaro Mateos, Claudia Pitzer, Christof Niehrs, Tansu Celikel, and Ana Martin-Villalba ; Cell Stem Cell 2013 (link)

5. Long-term channelrhodopsin-2 (ChR2) expression can induce abnormal axonal morphology and targeting in cerebral cortex Toshio Miyashita, Yu R. Shao, Jason Chung, Olivia Pourzia and Daniel E. Feldman ; Frontiers in Neural Circuits 2013 (link)

Common reaction to the title.

No but seriously. The poster on this work was at SFN this year. I felt a chill run up my spine whenever I walked by it 🙂

The most important words in the title are can induce , and thank goodness for that! If the can ran away and left behind simply induces the screams would be heard across the globe.

6. Signal Multiplexing and Single-Neuron Computations in Lateral Intraparietal Area During Decision-Making Miriam L. R. Meister, Jay A. Hennig, and Alexander C. Huk ; J Neuroscience 2013 (link)

7. Is Science Mostly Driven by Ideas or by Tools? Freeman J. Dyson ; Science 2012 (link)

This is not “hot off the presses” but this is one of my favorite issues to think about. I stumbled upon this paper via a quote from one of the F1000 commentaries on the paper here. The quote was, “…tools without ideas are a corpse; ideas without tools are a ghost.” from Ferdinando Boero. I like it.

8. Optopatcher—An electrode holder for simultaneous intracellular patch-clamp recording and optical manipulation Yonatan Katza, Ofer Yizhara, Jochen Staigerb, Ilan Lampla ; J Neuroscience Methods 2013 (link)

9. Differential Contribution of Hippocampal Circuits to Appetitive and Consummatory Behaviors during Operant Conditioning of Behaving Mice M. Teresa Jurado-Parras, Raudel Sa ́nchez-Campusano, Nazareth P. Castellanos, Francisco del-Pozo, Agne`s Gruart, and Jose ́ M. Delgado-García ; J Neuroscience 2013 (link)

10. Fast Computations in Cortical Ensembles Require Rapid Initiation of Action Potentials Vladimir Ilin, Aleksey Malyshev, Fred Wolf, and Maxim Volgushev ; J Neuroscience 2013 (link)

11. Pain-Specific Modulation of Hippocampal Activity and Functional Connectivity during Visual Encoding Katarina Forkmann, Katja Wiech, Christoph Ritter, Tobias Sommer, Michael Rose, and Ulrike Bingel ; J Neuroscience 2013 (link)

See below for something similar in rats.

12. Impaired Spatial Memory Performance in a Rat Model of Neuropathic Pain Is Associated with Reduced Hippocampus–Prefrontal Cortex Connectivity Helder Cardoso-Cruz, Deolinda Lima, and Vasco Galhardo ; J Neuroscience 2013 (link)

See above for something similar in humans.

13. Memory on time Howard Eichenbaum ; Trends in Cognitive Sciences 2013 (link)

Looks to be an interesting overview.

14. Pathfinding of Corticothalamic Axons Relies on a Rendezvous with Thalamic Projections Marie Deck, Ludmilla Lokmane, Sophie Chauvet, Caroline Mailhes, Maryama Keita, Mathieu Niquille, Michio Yoshida, Yutaka Yoshida, Ce ́ cile Lebrand, Fanny Mann, Elizabeth A. Grove, and Sonia Garel ; Neuron 2013 (link)

You know what I find to be one of the only things more mind blowing than the complexity of the brain? The fact that all of those cells and connections wire up themselves in development. I mean how insane is that?! (Answer: very insane)

Developmental Neuroscience: mind-blowing

Moving on…

These next two papers make a nice pair. The everlasting battle to classify neurons in the brain is no easy feat. I typically refer to the Markram review when thinking about interneuron diversity.

15. New insights into the classification and nomenclature of cortical GABAergic interneurons Javier DeFelipe, Pedro L. López-Cruz, Ruth Benavides-Piccione, Concha Bielza, Pedro Larrañaga, Stewart Anderson, Andreas Burkhalter, Bruno Cauli, Alfonso Fairén, Dirk Feldmeyer, Gord Fishell, David Fitzpatrick, Tamás F. Freund, Guillermo González-Burgos, Shaul Hestrin, Sean Hill, Patrick R. Hof, Josh Huang, Edward G. Jones, Yasuo Kawaguchi, Zoltán Kisvárday, Yoshiyuki Kubota, David A. Lewis, Oscar Marín, Henry Markram, Chris J. McBain, Hanno S. Meyer, Hannah Monyer, Sacha B. Nelson, Kathleen Rockland, Jean Rossier, John L. R. Rubenstein, Bernardo Rudy, Massimo Scanziani, Gordon M. Shepherd, Chet C. Sherwood, Jochen F. Staiger, Gábor Tamás, Alex Thomson, Yun Wang, Rafael Yuste and Giorgio A. Ascoli ; Nature Reviews Neuroscience 2013 (link)

16. Beyond the frontiers of neuronal types Demian Battaglia, Anastassios Karagiannis, Thierry Gallopin, Harold W. Gutch and Bruno Cauli ; Frontiers in Neural Circuits 2013 (link)

17. A BOLD statement about the hippocampal-neocortical dialogue Gyorgy Buzsaki and Adrien Peyrache ; Trends in Cognitive Sciences 2013 (link)

Nice commentary on a paper from a past post.

18. Gamma oscillations: precise temporal coordination without a metronome Danko Nikolic, Pascal Fries, and Wolf Singer ; Trends in Cognitive Sciences 2013 (link)

19. Cell-type-specific modulation of neocortical activity by basal forebrain input Henry J. Alitto and Yang Dan ; Frontiers in Systems Neuroscience 2013 (link)

19. Rat whisker motor cortex is subdivided into sensory-input and motor-output areas Jared B. Smith and Kevin D. Alloway ; Frontiers in Neural Circuits 2013 (link)

20. Vesicular stomatitis virus with the rabies virus glycoprotein directs retrograde transsynaptic transport among neurons in vivo Kevin T. Beier, Arpiar B. Saunders, Ian A. Oldenburg, Bernardo L. Sabatini and Constance L. Cepko ; Frontiers in Neural Circuits 2013 (link)

21. Spatial Modules of Coherent Activity in Pathway-Specific LFPs in the Hippocampus Reflect Topology and Different Modes of Presynaptic Synchronization N. Benito, A. Fernández-Ruiz, V.A. Makarov, J. Makarova, A. Korovaichuk and O. Herreras ; Cerebral Cortex 2013 (link)

22. Lateral entorhinal cortex is critical for novel object-context recognition David I.G. Wilson, Rosamund F. Langston, Magdalene I. Schlesiger, Monica Wagner, Sakurako Watanabe, James A. Ainge ; Hippocampus 2013 (link)

23. Lifetime memories from persistently supple synapses Aryeh Routtenberg ; Hippocampus 2013 (link)

This is an interesting commentary on memory theory. And below is a commentary on the commentary !

24. The conjunctive trace Blake A. Richards, Paul W. Frankland ; Hippocampus 2013 (link)

and last on the list…

25. Voltage sensitive dye imaging reveals shifting spatiotemporal spread of whisker-induced activity in rat barrel cortex Brian R Lustig, Robert M. Friedman, Jeremy E Winberry, Ford F Ebner, and Anna W Roe ; J Neurophysiology 2013 (link)

Friday Paper List February 1st

1. Short-Term Memory in Networks of Dissociated Cortical Neurons Mark R. Dranias, Han Ju, Ezhilarasan Rajaram, and Antonius M. J. VanDongen ; J Neuroscience 2013 (link)

This looks interesting. I’m not very familiar with the literature on dissociated cortical neural network studies, but it seems like a neat preparation to learn from.

2. Experience-dependent modification of a central amygdala fear circuit Haohong Li, Mario A Penzo, Hiroki Taniguchi, Charles D Kopec, Z Josh Huang & Bo Li ; Nature Neuroscience 2013 (link)

There have been a whole bunch of papers published (such as all four of these Deisseroth affiliated papers all published in Nature:  here, here, here, and here) showing optogenetic dissection of this amygdala circuitry and I am always blown away by how well they are able to specifically perturb such small individual targets. It’s really great stuff and I think this paper and the others previously published represent some of the best examples of the power of optogenetics to really tease apart functional circuitry.

3. Remapping of Border Ownership in the Visual Cortex Philip O’Herron and Rudiger von der Heydt ; J Neuroscience 2013 (link)

I love a good vision paper with an interesting/clever paradigm. I think this test of border ownership is really neat.

4. Biphasic Cholinergic Synaptic Transmission Controls Action Potential Activity in Thalamic Reticular Nucleus Neurons Yan-Gang Sun, Juan D. Pita-Almenar, Chia-Shan Wu, John J. Renger, Victor N. Uebele, Hui-Chen Lu, and Michael Beierlein ;  J Neuroscience 2013 (link)

5. Adaptation Improves Neural Coding Efficiency Despite Increasing Correlations in Variability Mehdi Adibi, James S. McDonald, Colin W. G. Clifford, and Ehsan Arabzadeh  ;  J Neuroscience 2013 (link)

I know of Ehsan Arabzadeh via his papers with Matthew Diamond. It looks like he is continuing to produce interesting, detailed work with thoughtful analysis.

6. Top-Down Modulation of Lateral Interactions in Visual Cortex Nirmala Ramalingam, Justin N.J. McManus, Wu Li, and Charles D. Gilbert ;  J Neuroscience 2013 (link)

7. Dense and Overlapping Innervation of Pyramidal Neurons by Chandelier Cells Melis Inan, Lidia Bla ́zquez-Llorca, Angel Mercha ́n-Pe ́rez, Stewart A. Anderson, Javier DeFelipe, and Rafael Yuste ;  J Neuroscience 2013 (link)

8. Memory, navigation and theta rhythm in the hippocampal-entorhinal system György Buzsáki & Edvard I Moser ; Nature Neuroscience 2013 (link)

I couldn’t be more excited about this review paper! This is wonderful!

9. Genetic identification of C fibres that detect massage-like stroking of hairy skin in vivo Sophia Vrontou, Allan M. Wong, Kristofer K. Rau, H. Richard Koerber & David J. Anderson ; Nature 2013 (link)

This looks like a really great paper that has it all: a really impressive preparation, sophisticated genetic specificity, and behavioral perturbations that demonstrate function. An exciting “general approach to the functional characterization of genetically identified subsets of somatosensory neurons in vivo” – what more can you want? 🙂

These next two papers come from a new online open-access journal that recently arrived called eLIFE !

There’s a new journal in town.

The journal is a “joint initiative of the Howard Hughes Medical Institute, the Max Planck Society, and the Wellcome Trust” that aims to become a model for a more efficient, open access, all digital publication. I really like the approach they are taking and hopefully they will be successful in shaking things up in the scientific publishing community. You can read about the journal here.

One neat feature that already caught my attention was the (optional) inclusion of the decision letter for the paper after the references. While I don’t see myself reading this for every paper, I think it’s a nice way to increase transparency in the review process.

10. Morphologic diversity of cutaneous sensory afferents revealed by genetically directed sparse labeling Hao Wu1, John Williams, Jeremy Nathans ; eLIFE 2013 (link)

11. Changing the responses of cortical neurons from sub- to suprathreshold using single spikes in vivo Verena Pawlak1, David S Greenberg, Henning Sprekeler, Wulfram Gerstner, Jason ND Kerr ; eLIFE 2013 (link)

12. Reactivation of Neural Ensembles during the Retrieval of Recent and Remote Memory Kaycie K. Tayler, Kazumasa Z. Tanaka, Leon G. Reijmers, and Brian J. Wiltgen ; Current Biology 2013 (link)

I haven’t had a chance to read this and see how it differs from the two big papers I mentioned in #2 of my Highlights of 2012 post but it’s great to see continued progress in the quest to pin down the “engram” and classical Hebbian neural ensembles.

13. Real-Time Visualization of Neuronal Activity during Perception Akira Muto, Masamichi Ohkura, Gembu Abe, Junichi Nakai,and Koichi Kawakami ; Current Biology 2013 (link)

There has already been a small explosion in the “popular press” on the internet talking about how this is the “first footage of thoughts being formed”. Of course this is far from the first time something like this has been done (for example check #3 from my Highlights of 2012 post). However I will say upfront this is some of the best signal and cleanest demonstration of real time imaging of activity I have seen. I mean just look at these two movies here and here. Watching the activity representing the paramecium dance across the retinotopy in the second movie is especially awesome!

14. Virtual Superheroes: Using Superpowers in Virtual Reality to Encourage Prosocial Behavior Robin S. Rosenberg, Shawnee L. Baughman, Jeremy N. Bailenson ; PLoS ONE 2013 (link)

This last paper is a step outside the usual stuff, but I had to include it for two reasons: a) I love comic books and superheroes b) I think sneaky behavioral tests are hilarious. I get a kick out of how after flying around as a superhero in virtual reality, the experimenter “accidentally” knocks over a cup of pens and then secretly measures if the subject helps pick them up. They even report how many pens the subjects pick up 🙂

“After completing the virtual task, the participant was taken out of the HMD and asked to have a seat in a chair nearby while the experimenter put away the virtual reality equipment. While the experimenter fumbled with the equipment, she “accidentally” knocked over a cup of 15 pens sitting on a table approximately four feet in front of the participant’s chair (Stage 2). The trained experimenter then waited five seconds before attempting to pick up the pens, giving the participant time to help. If the participant did not get up to help within those five seconds, the experimenter picked up the pens one at a time, still giving the participant the opportunity to help. See Figure 4A and 4B for photographs of the pens procedure. After the pen task was complete, the experimenter took the participant into a separate room to complete several questionnaires (Stage 3).”

Figure 4. The Experimenter Knocks Over The Pens And A Participant Kneels To Help Pick Up Pens.

This is why I don’t think I would make a good subject for a psych study. I would be extremely paranoid and constantly wondering if everything was a secret test. Then again, maybe that makes me perfect for a study on paranoia…
It appears that J. Neurophysiology (one of my favorite journals) has changed their publication schedule or something because to my surprise I just noticed that they put up a new issue online today!?

So that’s weird…

My world might be shattered… or it might be more difficult to post the paper list on Friday.. who knows.

So some last minute additions:

15. Circuit mechanisms revealed by spike-timing correlations in macaque area MT Xin Huang and Stephen G. Lisberger; J. Neurophysiology 2013 (link)

16. Updating of the spatial reference frame of head direction cells in response to locomotion in the vertical plane Jeffrey S. Taube, Sarah S. Wang, Stanley Y. Kim, and Russell J. Frohardt ; J. Neurophysiology 2013 (link)

This study looks pretty cool. The behavioral apparatus makes me dizzy just looking at it.

17. Effects of cortical feedback on the spatial properties of relay cells in the lateral geniculate nucleus Ian M. Andolina, Helen E. Jones, and Adam M. Sillito ; J. Neurophysiology 2013 (link)

Alright that should do it. List done.