Friday Paper Post – Posted Thursday May 21st

That time of the year again. The birthday of the man himself :

 

I’m very sorry I have fallen so far behind. I can’t believe this is my first paper post in 2015.

Cheer up though, there are plenty of great papers to catch up on!

Just a few from the pile. Since most are from much earlier in the year. You might remember seeing them when they came out, but now you can get around to reading themūüôā

Let’s see how long it will take to catch back up to posting about the most current stuff…

1) Internal models direct dragonfly interception steering Matteo Mischiati, Huai-Ti Lin, Paul Herold, Elliot Imler, Robert Olberg & Anthony Leonardo ; Nature 2015 (link)

2) Three-dimensional head-direction coding in the bat brain Arseny Finkelstein , Dori Derdikman, Alon Rubin, Jakob N. Foerste, Liora Las & Nachum Ulanovsky; Nature 2015 (link)

3) Mechanosensory interactions drive collective behaviour in Drosophila Pavan Ramdya, Pawel Lichocki, Steeve Cruchet, Lukas Frisch, Winnie Tse, Dario Floreano & Richard Benton; Nature 2015 (link)

4) Orientation columns in the mouse superior colliculus Evan H. Feinberg & Markus Meister; Nature 2015 (link)

5) Optogenetic control of organelle transport and positioning Petra van Bergeijk, Max Adrian, Casper C. Hoogenraad & Lukas C. Kapitein ; Nature 2015 (link)

6) Distinct relationships of parietal and prefrontal cortices to evidence accumulation Timothy D. Hanks, Charles D. Kopec, Bingni W. Brunton, Chunyu A. Duan, Jeffrey C. Erlich & Carlos D. Brody ; Nature 2015 (link)

7) Emotional learning selectively and retroactively strengthens memories for related events Joseph E. Dunsmoor, Vishnu P. Murty, Lila Davachi & Elizabeth A. Phelps; Nature 2015 (link)

8) A direct GABAergic output from the basal ganglia to frontal cortex Arpiar Saunders, Ian A. Oldenburg, Vladimir K. Berezovskii, Caroline A. Johnson, Nathan D. Kingery, Hunter L. Elliott, Tiao Xie, Charles R. Gerfen & Bernardo L. Sabatini ; Nature 2015 (link)

9) Shearing-induced asymmetry in entorhinal grid cells Tor Stensola, Hanne Stensola, May-Britt Moser & Edvard I. Moser ; Nature 2015 (link)

10) Grid cell symmetry is shaped by environmental geometry Julija Krupic, Marius Bauza, Stephen Burton, Caswell Barry & John O’Keefe ; Nature 2015 (link)

11) Neural correlates of strategic reasoning during competitive games Hyojung Seo,Xinying Cai, Christopher H. Donahue, Daeyeol Lee ; Science 2015 (link)

12)¬†Electronic dura mater for long-term multimodal neural interfaces Ivan R. Minev, Pavel Musienko, Arthur Hirsch, Quentin Barraud, Nikolaus Wenger, Eduardo Martin Moraud, JeŐĀroŐāme Gandar, Marco Capogrosso, Tomislav Milekovic, LeŐĀonie Asboth, Rafael Fajardo Torres, Nicolas Vachicouras, Qihan Liu, Natalia Pavlova, Simone Duis, Alexandre Larmagnac, Janos VoŐąroŐąs, Silvestro Micera, Zhigang Suo, GreŐĀgoire Courtine, SteŐĀphanie P. Lacour ;¬†Science 2015 (link)

13) Number-space mapping in the newborn chick resembles humans’ mental number line Rosa Rugani, Giorgio Vallortigara, Konstantinos Priftis, Lucia Regolin ; Science 2015 (link)

14)¬†Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq Amit Zeisel, Ana B. MunŐÉoz Manchado, Simone Codeluppi, Peter LoŐąnnerberg, Gioele La Manno, Anna JureŐĀus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz, Charlotte Rolny, GoncŐßalo Castelo-Branco, Jens Hjerling-Leffler, Sten Linnarsson ;¬†Science 2015 (link)

15)¬†Refining deep brain stimulation to emulate optogenetic treatment of synaptic pathology Meaghan Creed, Vincent Jean Pascoli, Christian LuŐąscher¬†;¬†Science 2015 (link)

16) Expansion microscopy Fei Chen, Paul W. Tillberg, Edward S. Boyden ; Science 2015 (link)

17) Theta sequences are essential for internally generated hippocampal firing fields Yingxue Wang, Sandro Romani, Brian Lustig, Anthony Leonardo & Eva Pastalkova ; Nature Neuroscience 2015 (link)

18) A genetically specified connectomics approach applied to long-range feeding regulatory circuits Deniz Atasoy, J Nicholas Betley, Wei-Ping Li, Helen H Su, Sinem M Sertel, Louis K Scheffer, Julie H Simpson, Richard D Fetter & Scott M Sternson ; Nature Neuroscience 2015 (link)

19) Novel domain formation reveals proto-architecture in inferotemporal cortex Krishna Srihasam, Justin L Vincent & Margaret S Livingstone ; Nature Neuroscience 2015 (link)

20) A category-free neural population supports evolving demands during decision-making David Raposo, Matthew T Kaufman & Anne K Churchland ; Nature Neuroscience 2015 (link)

21) A hierarchy of intrinsic timescales across primate cortex John D Murray, Alberto Bernacchia, David J Freedman, Ranulfo Romo, Jonathan D Wallis, Xinying Cai, Camillo Padoa-Schioppa, Tatiana Pasternak, Hyojung Seo, Daeyeol Lee & Xiao-Jing Wang ; Nature Neuroscience 2014 (link)

22 ) Impaired spatial selectivity and intact phase precession in two-dimensional virtual reality Zahra M Aghajan, Lavanya Acharya, Jason J Moore, Jesse D Cushman, Cliff Vuong & Mayank R Mehta ; Nature Neuroscience 2015 (link)

23) Columnar organization of spatial phase in visual cortex Yushi Wang, Jianzhong Jin, Jens Kremkow, Reza Lashgari, Stanley J Komban & Jose M Alonso ; Nature Neuroscience 2015 (link)

24) A learning-based approach to artificial sensory feedback leads to optimal integration Maria C Dadarlat, Joseph E O’Doherty & Philip N Sabes ; Nature Neuroscience 2015 (link)

25) Spatially Selective Holographic Photoactivation and Functional Fluorescence Imaging in Freely Behaving Mice with a Fiberscope Vivien Szabo, Cathie Ventalon, Vincent De Sars, Jonathan Bradley, and Valentina Emiliani ; Neuron 2015 (link)

26)¬†Visualization of NMDA receptor‚Äďdependent AMPA receptor synaptic plasticity in vivo Yong Zhang, Robert H Cudmore, Da-Ting Lin, David J Linden & Richard L Huganir¬†;¬†Nature Neuroscience¬†2015 (link)

27) The neocortical circuit: themes and variations Kenneth D Harris & Gordon M G Shepherd ; Nature Neuroscience 2015 (link)

28) Visual recognition memory, manifested as long-term habituation, requires synaptic plasticity in V1 Sam F Cooke, Robert W Komorowski, Eitan S Kaplan, Jeffrey P Gavornik & Mark F Bear ; Nature Neuroscience 2015 (link)

29) The development of cortical circuits for motion discrimination Gordon B Smith, Audrey Sederberg, Yishai M Elyada, Stephen D Van Hooser, Matthias Kaschube & David Fitzpatrick ; Nature Neuroscience 2015 (link)

30)¬†NeuroGrid: recording action potentials from the surface of the brain Dion Khodagholy, Jennifer N Gelinas, Thomas Thesen, Werner Doyle, Orrin Devinsky, George G Malliaras & GyoŐąrgy BuzsaŐĀki¬†;¬†Nature Neuroscience¬†2014¬†(link)

31) Simultaneous cellular-resolution optical perturbation and imaging of place cell firing fields John Peter Rickgauer, Karl Deisseroth & David W Tank ; Nature Neuroscience 2014 (link)

32) Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo Adam M Packer, Lloyd E Russell, Henry W P Dalgleish & Michael HaŐąusser¬†;¬†Nature Neuroscience¬†2014¬†(link)

 

 

It has been a long time

It has been so long. I am so behind…

mygodfullofstars

 

I have so many papers to post that it is overwhelming. Plus I know everyone is hanging on the edge of their collective seats begging for me to post my list of the top papers from 2014!ūüėõ

However, in the mean time I cannot possibly resist directing everyone towards a great blog post from DrugMonkey.

You absolutely must read this wonderful, provocative blog post!

 

I just love so much about this post. I loved being scandalized when I realized I had completely forgotten about the subfornical control of drinking lessons from biology classes in the past.

But please don’t stop with the post itself. The continued¬†discussion in the comments is even better!! So good!!!!

I love the comments about optogenetics.

Let me be clear – I have mentioned before I am a huge Optogenetics Fan – I constantly strive to make everything I do in science linked with optogenetics. If I could, I would have my entire lifestyle saturated with the glorious method. I would ride from place to place on a sled pulled by thousands of cre-rats with ChR2 in their motor cortex… but I wont get carried away.

The point is as much as I love optogenetics, I also really enjoy when people question the use of the method. I like when people point out the limitations; how important certain controls are; or when optogenetics is used wrong.

But even better than the optogenetics discussion is the underlying point about science publishing and the glorified status of Nature and Science. I know I have said that I am passionate about the flaws in our science publishing system before, but I like the points that are brought up in the commentary especially from rxnm.

One of the things that makes me so frustrated about science publishing is not just the often talked about money madness, but how the ridiculous weight we give to these journals allows them to essentially dictate the direction of science itself. I hate the fact that getting a¬†Nature or¬†Science paper can make or break an entire career in science – jobs, funding, etc.. When this ultimately manifests into a situation where¬†an editor for a magazine is given the power to determine what is and isn’t valuable science. Of course… this discussion is very nuanced and I could go on, but I’ll stop while I can.

Anyway I have to at least repost the one comment from rxnm ,

“Nature is a private company, they can publish whatever the fuck they want and sell the ad space next to it. The chumps are the people who admire a paper because it’s published there. Believing that NPG’s primary goal is rigorous scientific standards instead of whatever is splashy and marketable is like believing Facebook is here to try to bring people closer together and make the world a better place.”

So great! I just love it!

 

Anyway if you still haven’t, please do check out the blog post and the comments here. I hope you enjoy it as much as I do.

I have no idea when.. but hopefully I’ll post some papers sometime in the next ten yearsūüôā

 

 

 

Friday Paper Post – Friday Oct. 31st

Happy Halloween!

Still catching up. Most of these papers are from around August. Hopefully I can get an extra post in soon so we can be caught back up to the latest and greatest each weekūüôā

1) Sensory-evoked LTP driven by dendritic plateau potentials in vivo Frederic Gambino, Stephane Pages, Vassilis Kehayas, Daniela Baptista, Roberta Tatti, Alan Carleton & Anthony Holtmaat ; Nature 2014 (link)

  • I enjoyed this paper!

2) A synaptic and circuit basis for corollary discharge in the auditory cortex ¬†ÔŅľÔŅľÔŅľDavid M. Schneider, Anders Nelson & Richard Mooney¬†;¬†Nature 2014 (link)

  • Sound processing takes motor control Uri Livneh & Anthony Zador¬†¬†;¬†Nature 2014 (link)

3) Neural constraints on learning Patrick T. Sadtler, Kristin M. Quick, Matthew D. Golub, Steven M. Chase, Stephen I. Ryu, Elizabeth C. Tyler-Kabara, Byron M. Yu & Aaron P. Batista ; Nature 2014 (link)

4) Bidirectional switch of the valence associated with a hippocampal contextual memory engram Roger L. Redondo, Joshua Kim, Autumn L. Arons, Steve Ramirez, Xu Liu & Susumu Tonegawa ; Nature 2014 (link)

  • Shedding light on a change of mind¬†Tomonori Takeuchi W & Richard G. M. Morris¬†;¬†Nature 2014 (link)
  • This is essentially the third paper in a series of optogenetic manipulations of the engram from the Tonegawa lab.

5) State-Dependent Architecture of Thalamic Reticular Subnetworks Michael M. Halassa, Zhe Chen, Ralf D. Wimmer, Philip M. Brunetti, Shengli Zhao, Basilis Zikopoulos, Fan Wang, Emery N. Brown, and Matthew A. Wilson ; Cell 2014 (link)

  • I want to especially recommend this paper! I thought it was pretty fantastic and it will definitely make¬†my list of top papers of the year. So yeah, check out this paper!
  • Also hard to know if this is available without access to Cell.. but if you can get to this link here – you can click on the tab that says “PaperFlick”¬†behind the picture I posted above and watch a short little movie about the paper.

6)¬†Circadian Pacemaker Neurons Change Synaptic Contacts across the Day E. Axel Gorostiza, Ana Depetris-Chauvin, Lia Frenkel, Nicolas PńĪrez, and MarńĪa Fernanda Ceriani ;¬†Current Biology 2014 (link)

7) The Stimulus Selectivity and Connectivity of Layer Six Principal Cells Reveals Cortical Microcircuits Underlying Visual Processing Mateo Velez-Fort, Charly V. Rousseau, Christian J. Niedworok, Ian R. Wickersham, Ede A. Rancz, Alexander P.Y. Brown, Molly Strom, and Troy W. Margrie ; Neuron 2014 (link)

8) Segregation of Tactile Input Features in Neurons of the Cuneate Nucleus Henrik Jorntell, Fredrik Bengtsson, Pontus Geborek, Anton Spanne, Alexander V. Terekhov, and Vincent Hayward ; Neuron 2014 (link)

9) Sparseness and Expansion in Sensory Representations Baktash Babadi and Haim Sompolinsky ; Neuron 2014 (link)

10) Visual Stimulation Switches the Polarity of Excitatory Input to Starburst Amacrine Cells Anna L. Vlasits, Remi Bos, Ryan D. Morrie, Cecile Fortuny, John G. Flannery, Marla B. Feller, and Michal Rivlin-Etzion ; Neuron 2014 (link)

11) Multisensory Integration in the Mouse Striatum Ramon Reig and Gilad Silberberg ; Neuron 2014 (link)

12) Can We Reconcile the Declarative Memory and Spatial Navigation Views on Hippocampal Function? Howard Eichenbaum and Neal J. Cohen ; Neuron 2014 (link)

13) Gamma-range synchronization of fast-spiking interneurons can enhance detection of tactile stimuli Joshua H Siegle, Dominique L Pritchett & Christopher I Moore ; Nature Neuroscience 2014 (link)

14) Reversal of theta rhythm flow through intact hippocampal circuits Jesse Jackson, BeŐĀneŐĀdicte Amilhon, Romain Goutagny, Jean-Bastien Bott, FreŐĀdeŐĀric Manseau, Christian Kortleven, Steven L Bressler & Sylvain Williams¬†;¬†Nature Neuroscience 2014 (link)

15) Edge-orientation processing in first-order tactile neurons J Andrew Pruszynski & Roland S Johansson ; Nature Neuroscience 2014 (link)

16) Multiplexed aberration measurement for deep tissue imaging in vivo Chen Wang, Rui Liu, Daniel E Milkie, Wenzhi Sun, Zhongchao Tan, Aaron Kerlin, Tsai-Wen Chen, Douglas S Kim & Na Ji ; Nature Methods 2014 (link)

17) A suppression hierarchy among competing motor programs drives sequential grooming in Drosophila Andrew M Seeds, Primoz Ravbar, Phuong Chung, Stefanie Hampel, Frank M Midgley Jr, Brett D Mensh, Julie H Simpson ; eLife 2014 (link)

18) Interlamellar CA1 network in the hippocampus Sunggu Yang, Sungchil Yang, Thais Moreira, Gloria Hoffman, Greg C. Carlson, Kevin J. Bender, Bradley E. Alger, and Cha-Min Tang ; PNAS 2014 (link)

19)¬†Optogenetic activation of septal cholinergic neurons suppresses sharp wave ripples and enhances theta oscillations in the hippocampus Marie Vandecasteele, Viktor Varga, Antal BereŐĀnyi,, Edit Papp, PeŐĀter BarthoŐĀ, Laurent Venance, TamaŐĀs F. Freund, and GyoŐąrgy BuzsaŐĀki ;¬†PNAS 2014 (link)

20) Acetylcholine functionally reorganizes neocortical microcircuits Melissa J. Runfeldt, Alexander J. Sadovsky, and Jason N. MacLean ; JNeurophys 2014 (link)

21) Mechanisms of Sharp Wave Initiation and Ripple Generation Daniel Schlingloff,  Szabolcs Kali, Tamas F. Freund, Norbert Hajos, and  Attila I. Gulyas ; JNeurosci 2014 (link)

22) Correlations in V1 Are Reduced by Stimulation Outside the Receptive Field  Adam C. Snyder, Michael J. Morais, Adam Kohn, and  Matthew A. Smith ; JNeurosci 2014 (link)

23) Frequency-Dependent, Cell Type-Divergent Signaling in the Hippocamposeptal Projection Joanna Mattis, Julia Brill, Suzanne Evans, Talia N. Lerner,  Thomas J. Davidson, Minsuk Hyun,  Charu Ramakrishnan, Karl Deisseroth, and John R. Huguenard ; JNeurosci 2014 (link)

24) Beta Oscillation Dynamics in Extrastriate Cortex after Removal of Primary Visual Cortex  Joscha T. Schmiedt,  Alexander Maier, Pascal Fries, Richard C. Saunders,  David A. Leopold, and Michael C. Schmid ; JNeurosci 2014 (link)

25) Conscious Brain-to-Brain Communication in Humans Using Non-Invasive Technologies Carles Grau, Romuald Ginhoux, Alejandro Riera, Thanh Lam Nguyen, Hubert Chauvat, Michel Berg, Julia L. Amengual, Alvaro Pascual-Leone, Giulio Ruffini ; PLoS One 2014 (link)

  • also known as “talking” ¬†ūüėõ

 

 

Friday Paper Post – Friday October 24th 2014

This blog will continue hobbling along until the posts are caught up.

Here are more papers from over the summer!

1)¬†Fast-spiking, parvalbumin+ GABAergic interneurons: From cellular design to microcircuit function ÔŅľ Hua Hu, Jian Gan, Peter Jonas;¬†Science 2014 (link)

2) Long-range and local circuits for top-down modulation of visual cortex processing Siyu Zhang, Min Xu, Tsukasa Kamigaki, Johnny Phong Hoang Do, Wei-Cheng Chang, Sean Jenvay, Kazunari Miyamichi, Liqun Luo, Yang Dan ; Science 2014 (link)

3) Large environments reveal the statistical structure governing hippocampal representations P. Dylan Rich, Hua-Peng Liaw, Albert K. Lee; Science 2014 (link)

  • Well done Dr. Richūüôā

4) A memory of errors in sensorimotor learning David J. Herzfeld, Pavan A. Vaswani, Mollie Marko, Reza Shadmehr ; Science 2014 (link)

5) A million spiking-neuron integrated circuit with a scalable communication network and interface Paul A. Merolla, John V. Arthur, Rodrigo Alvarez-Icaza, Andrew S. Cassidy, Jun Sawada, Filipp Akopyan, Bryan L. Jackson, Nabil Imam, Chen Guo, Yutaka Nakamura, Bernard Brezzo, Ivan Vo, Steven K. Esser, Rathinakumar Appuswamy, Brian Taba, Arnon Amir, Myron D. Flickner, William P. Risk, Rajit Manohar, Dharmendra S. Modha ; Science 2014 (link)

6) Forebrain Engraftment by Human Glial Progenitor Cells Enhances Synaptic Plasticity and Learning in Adult Mice Xiaoning Han, Michael Chen, Fushun Wang, Martha Windrem, Su Wang, Steven Shanz, Qiwu Xu, Nancy Ann Oberheim, Lane Bekar, Sarah Betstadt, Alcino J. Silva, Takahiro Takano, Steven A. Goldman, and Maiken Nedergaard ; Cell 2014 (link)

7) Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing Bin Yang, Jennifer B. Treweek, Rajan P. Kulkarni, Benjamin E. Deverman, Chun-Kan Chen, Eric Lubeck, Sheel Shah, Long Cai, and Viviana Gradinaru ; Cell 2014 (link)

8) Through-skull fluorescence imaging of the brain in a new near-infrared window Guosong Hong, Shuo Diao, Junlei Chang, Alexander L. Antaris, Changxin Chen, Bo Zhang, Su Zhao, Dmitriy N. Atochin, Paul L. Huang, Katrin I. Andreasson, Calvin J. Kuo and Hongjie Dai ; Nature Photonics 2014 (link)

9)¬†Self-Generated Movements with ‚Äė‚ÄėUnexpected‚Äô‚Äô Sensory Consequences Alexandre Tiriac, Carlos Del Rio-Bermudez, and Mark S. Blumberg ;¬†Current Biology 2014 (link)

10)¬†Astrocytes contribute to gamma oscillations and recognition memory Hosuk Sean Lee, Andrea Ghetti, AntoŐĀnio Pinto-Duarte, Xin Wang, Gustavo Dziewczapolskia, Francesco Galimi, Salvador Huitron-Resendiz, Juan C. PinŐÉa-Crespo, Amanda J. Roberts, Inder M. Verma, Terrence J. Sejnowski, and Stephen F. Heinemann ;¬†PNAS 2014 (link)

11) Neurons Are Recruited to a Memory Trace Based on Relative Neuronal Excitability Immediately before Training Adelaide P. Yiu,Valentina Mercaldo, Chen Yan, Blake Richards, Asim J. Rashid, Hwa-Lin Liz Hsiang, Jessica Pressey, Vivek Mahadevan, Matthew M. Tran, Steven A. Kushner, Melanie A. Woodin, Paul W. Frankland, and Sheena A. Josselyn ; Nature Neuroscience 2014 (link)

12)¬†‚ÄėSilent‚Äô mitral cells dominate odor responses in the olfactory bulb of awake mice Mihaly Kollo, Anja Schmaltz, Mostafa Abdelhamid, Izumi Fukunaga & Andreas T Schaefer¬†;¬†Nature Neuroscience 2014¬†(link)

13)¬†Cerebellum involvement in cortical sensorimotor circuits for the control of voluntary movements ReŐĀmi D Proville, Maria Spolidoro, Nicolas Guyon, Guillaume P DugueŐĀ, Fekrije Selimi, Philippe Isope, Daniela Popa & CleŐĀment LeŐĀna¬†;¬†Nature Neuroscience 2014¬†(link)

14) Anterior cingulate engagement in a foraging context reflects choice difficulty, not foraging value Amitai Shenhav, Mark A Straccia, Jonathan D Cohen & Matthew M Botvinick ; Nature Neuroscience 2014 (link)

15) An olfactory cocktail party: figure-ground segregation of odorants in rodents Dan Rokni, Vivian Hemmelder, Vikrant Kapoor & Venkatesh N Murthy ; Nature Neuroscience 2014 (link)

16) A comprehensive thalamocortical projection map at the mesoscopic level Barbara J Hunnicutt, Brian R Long, Deniz Kusefoglu, Katrina J Gertz, Haining Zhong & Tianyi Mao ; Nature Neuroscience 2014 (link)

17) Direct and indirect pathways of basal ganglia: a critical reappraisal Paolo Calabresi, Barbara Picconi, Alessandro Tozzi, Veronica Ghiglieri & Massimiliano Di Filippo ; Nature Neuroscience 2014 (link)

18) Dynamic circuit motifs underlying rhythmic gain control, gating and integration Thilo Womelsdorf, Taufik A Valiante, Ned T Sahin, Kai J Miller & Paul Tiesinga ; Nature Neuroscience 2014 (link)

19) Multiscale Optical Ca2+ Imaging of Tonal Organization in Mouse Auditory Cortex John B. Issa, Benjamin D. Haeffele, Amit Agarwal, Dwight E. Bergles, Eric D. Young, and David T. Yue ; Neuron 2014 (link)

20) Enhancement of encoding and retrieval functions through theta phase-specific manipulation of hippocampus Joshua H Siegle, Matthew A Wilson ; eLife 2014 (link)

  • I was very excited about this paper. If you aren’t familiar with Josh Siegle and his work¬†as a founder of¬†Open Ephys, then I highly recommend checking it out here.

21)¬†Nucleus reuniens of the thalamus contains head direction cells Maciej M Jankowski, Md N Islam, Nicholas F Wright, Seralynne D Vann, Jonathan T Erichsen, John P Aggleton, Shane M O’Mara¬†; eLife 2014¬†(link)

22) Mapping brain activity at scale with cluster computing Jeremy Freeman, Nikita Vladimirov, Takashi Kawashima, Yu Mu, Nicholas J Sofroniew, Davis V Bennett, Joshua Rosen, Chao-Tsung Yang, Loren L Looger & Misha B Ahrens ; Nature Methods 2014 (link)

23)¬†Deep brain optical measurements of cell type‚Äď specific neural activity in behaving mice Guohong Cui, Sang Beom Jun, Xin Jin, Guoxiang Luo, Michael D Pham, David M Lovinger, Steven S Vogel & Rui M Costa ;¬†Nature Protocols 2014 (link)

24) Advanced CLARITY for rapid and high-resolution imaging of intact tissues Raju Tomer, Li Ye, Brian Hsueh & Karl Deisseroth ; Nature Protocols 2014 (link)

25) Visual Categorization of Natural Movies by Rats Kasper Vinken, Ben Vermaercke, and Hans P. Op de Beeck ; J Neurosci 2014 (link)

26) Cellular mechanisms for response heterogeneity among L2/3 pyramidal cells in whisker somatosensory cortex Justin Elstrott, Kelly B. Clancy, Haani Jafri, Igor Akimenko, and Daniel E. Feldman; J Neurophys 2014 (link)

27)¬†Induced Neural Stem Cells Achieve Long-Term Survival and Functional Integration in the Adult Mouse Brain Kathrin Hemmer, Mingyue Zhang, Thea van Wu Őąllen, Marna Sakalem, Natalia Tapia, Aidos Baumuratov, Christian Kaltschmidt, Barbara Kaltschmidt, Hans R. Scholer, Weiqi Zhang, and Jens C. Schwamborn ;¬†Stem Cell Reports 2014 (link)

28) Direct 3D Analyses Reveal Barrel-Specific Vascular Distribution and Cross-Barrel Branching in the Mouse Barrel Cortex Jingpeng Wu, Congdi Guo, Shangbin Chen, Tao Jiang, Yong He, Wenxiang Ding, Zhongqin Yang, Qingming Luo and Hui Gong ; Cerebral Cortex 2014 (link)

29) Intact CA3 in the Hippocampus is Only Sufficient for Contextual Behavior Based on Well-Learned and Unaltered Visual Background Jae-Rong Ahn and Inah Lee ; Hippocampus 2014 (link)

30) The Visual Microphone: Passive Recovery of Sound from Video Abe Davis, Michael Rubinstein, Neal Wadhwa, Gautham J. Mysore, Fredo Durand, William T. Freeman ; SIGGRAPH 2014 (link)

Friday Paper Post – Friday Oct. 17th

You may have¬†thought I fell asleep and forgot to make blog posts forever…

Don’t worry I’m awakeūüôā

More papers catching up from the summer. These are mostly from late June and early July. Enjoy!

1) Processing properties of ON and OFF pathways for Drosophila motion detection Rudy Behnia, Damon A. Clark, Adam G. Carter, Thomas R. Clandinin & Claude Desplan ; Nature 2014 (link)

2) Optical Neural Interfaces Melissa R. Warden, Jessica A. Cardin, and Karl Deisseroth ; Ann Rev Biomed Eng 2014 (link)

3)¬†Noninvasive optical inhibition with a red-shifted microbial rhodopsin Amy S Chuong, Mitra L Miri, Volker Busskamp, Gillian A C Matthews, Leah C Acker, Andreas T S√łrensen, Andrew Young, Nathan C Klapoetke, Mike A Henninger, Suhasa B Kodandaramaiah, Masaaki Ogawa, Shreshtha B Ramanlal, Rachel C Bandler, Brian D Allen, Craig R Forest, Brian Y Chow, Xue Han, Yingxi Lin, Kay M Tye, Botond Roska, Jessica A Cardin & Edward S Boyden ;¬†Nature Neuroscience 2014 (link)

  • I was excited about this paper.

4) Independent control of gamma and theta activity by distinct interneuron networks in the olfactory bulb Izumi Fukunaga, Jan T Herb, Mihaly Kollo, Edward S Boyden & Andreas T Schaefer ; Nature Neuroscience 2014 (link)

5) Reactivation of emergent task-related ensembles during slow-wave sleep after neuroprosthetic learning Tanuj Gulati, Dhakshin S Ramanathan, Chelsea C Wong & Karunesh Ganguly ; Nature Neuroscience 2014 (link)

6) Simultaneous transcranial magnetic stimulation and single-neuron recording in alert non-human primates Jerel K Mueller, Erinn M Grigsby, Vincent Prevosto, Frank W Petraglia III, Hrishikesh Rao, Zhi-De Deng, Angel V Peterchev, Marc A Sommer, Tobias Egner, Michael L Platt & Warren M Grill ; Nature Neuroscience 2014 (link)

7) Differences in the emergent coding properties of cortical and striatal ensembles Liya Ma, James M Hyman, Adrian J Lindsay, Anthony G Phillips & Jeremy K Seamans ; Nature Neuroscience 2014 (link)

8) Increases in Functional Connectivity between Prefrontal Cortex and Striatum during Category Learning Evan G. Antzoulatos and Earl K. Miller ; Neuron 2014 (link)

9) A Model of Grid Cell Development through Spatial Exploration and Spike Time-Dependent Plasticity John Widloski and Ila R. Fiete ; Neuron 2014 (link)

10) Eye Movement Preparation Modulates Neuronal Responses in Area V4 When Dissociated from Attentional Demands Nicholas A. Steinmetz and Tirin Moore ; Neuron 2014 (link)

11) Identification of a Brainstem Circuit Regulating Visual Cortical State in Parallel with Locomotion A. Moses Lee, Jennifer L. Hoy, Antonello Bonci, Linda Wilbrecht, Michael P. Stryker, and Cristopher M. Niell ; Neuron 2014 (link)

12) Pyramidal Cell-Interneuron Interactions Underlie Hippocampal Ripple Oscillations Eran Stark, Lisa Roux, Ronny Eichler, Yuta Senzai, Sebastien Royer, and Gyorgy Buzsaki  ; Neuron 2014 (link)

  • I like how this paper frames itself as distinguishing between the four possible network models in figure 1.

13) Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites Douglas J. Bakkum, Urs Frey, Milos Radivojevic, Thomas L. Russell, Jan Muller, Michele Fiscella, Hirokazu Takahashi & Andreas Hierlemann ; Nature Communications 2014 (link)

14) idTracker: tracking individuals in a group by automatic identification of unmarked animals Alfonso Pérez-Escudero, Julián Vicente-Page, Robert C Hinz, Sara Arganda & Gonzalo G de Polavieja ; Nature Methods 2014 (link)

  • Distinguishing seemingly indistinguishable animals with computer vision Kristin Branson ;¬†Nature Methods 2014¬†(link)

15)¬†Activation and measurement of free whisking in the lightly anesthetized rodent Jeffrey D Moore, Martin DescheŐānes, Anastasia Kurnikova & David Kleinfeld ;¬†Nature Protocols¬†2014 (link)

16) Object-Centered Shifts of Receptive Field Positions in Monkey Primary Visual Cortex Amy M. Ni, Scott O. Murray, and Gregory D. Horwitz ; Current Biology 2014 (link)

17) Experimental evidence of massive-scale emotional contagion through social networks Adam D. I. Kramer, Jamie E. Guillory, and Jeffrey T. Hancock ; PNAS 2014 (link)

  • If I remember correctly there was a big hullabaloo in the press about this paper and the involvement of Facebook.

18) Recovery of consciousness is mediated by a network of discrete metastable activity states Andrew E. Hudson, Diany Paola Calderon, Donald W. Pfaff, and Alex Proekt ; PNAS 2014 (link)

19) When recognition memory is independent of hippocampal function Christine N. Smith, Annette Jeneson, Jennifer C. Frascino, C. Brock Kirwan, Ramona O. Hopkins, and Larry R. Squire ; PNAS 2014 (link)

20) Activity-dependent dendritic spine neck changes are correlated with synaptic strength Roberto Araya, Tim P. Vogels, and Rafael Yuste ; PNAS 2014 (link)

21) Sparse and distributed coding of episodic memory in neurons of the human hippocampus John T. Wixted, Larry R. Squire, Yoonhee Jang, Megan H. Papesh, Stephen D. Goldingerg, Joel R. Kuhn, Kris A. Smith, David M. Treiman, and Peter N. Steinmetz ; PNAS 2014 (link)

22) Natural Whisker-Guided Behavior by Head-Fixed Mice in Tactile Virtual Reality Nicholas J. Sofroniew, Jeremy D. Cohen, Albert K. Lee, and Karel Svoboda ; JNeurosci 2014 (link)

  • A well done paper from Dr. Sofroniew.

23) Layer 6 Corticothalamic Neurons Activate a Cortical Output Layer, Layer 5a Juhyun Kim, Chanel J. Matney, Aaron Blankenship, Shaul Hestrin, and X Solange P. Brown ; JNeurosci 2014 (link)

24)¬†New Insights into the Role of Respiratory Inputs in Hippocampal Oscillations Andre ŐĀ L.V. Lockmann and Hindiael Belchior¬†;¬†JNeurosci 2014 (link)

25) Emergence of Feature-Specific Connectivity in Cortical Microcircuits in the Absence of Visual Experience X Ho Ko, Thomas D. Mrsic-Flogel, and Sonja B. Hofer ; JNeurosci 2014 (link)

26) Laserspritzer: A Simple Method for Optogenetic Investigation with Subcellular Resolutions Qian-Quan Sun, Xinjun Wang, Weiguo Yang ; PLoS One 2014 (link)

27) Paired stimulation between CA3 and CA1 alters excitability of CA3 in the rat hippocampus Hiroyuki Ohta, Seiichiro Sakai, Shin Ito Toru Ishizuka, Yugo Fukazawa, Takehito Kemuriyama, Megumi Tandai-Hiruma, Hajime Mushiake, Yoshiaki Sato, Hiromu Yawo, Yasuhiro Nishida ; Neuroscience Letters 2014 (link)

28) Extraction of optical properties and prediction of light distribution in rat brain tissue Mehdi Azimipour, Ryan Baumgartner, Yuming Liu, Steven L. Jacques, Kevin Eliceiri, and Ramin Pashaie : Journal of BioMed Optics 2014 (link)

29) Human brain lesion-deficit inference remapped Yee-Haur Mah, Masud Husain, Geraint Rees and Parashkev Nachev ; Brain 2014 (link)

30) Electrical stimulation of a small brain area reversibly disrupts consciousness Mohamad Z. Koubeissi , Fabrice Bartolomei , Abdelrahman Beltagy , Fabienne Picard ; Epilepsy and Behavior 2014 (link)

 

Friday Paper Post – Sunday October 12th

Wow…. So summer happened… and more.

Very behind on posting. So far behind that my folders of papers resemble the picture on the top of the blog.

The only possible way to even attempt to get caught up is going to involve breaking these papers down into months missed. Otherwise this post would be over 100 papers long.

Many good papers and exciting developments over the past few months as well. Hopefully I will get a chance to comment on them.

Some papers from June below:

1)¬†Equalizing excitation‚Äďinhibition ratios across visual cortical neurons Mingshan Xue, Bassam V. Atallah & Massimo Scanziani ;¬†Nature 2014 (link)

2) Distinct Lineage-Dependent Structural and Functional Organization of the Hippocampus Hua-Tai Xu, Zhi Han, Peng Gao, Shuijin He, Zhizhong Li, Wei Shi, Oren Kodish, Wei Shao, Keith N. Brown, Kun Huang, and Song-Hai Shi ; Cell 2014 (link)

  • Assembling Cell Ensembles Nelson Spruston;¬†Cell 2014¬†(link)

3) Natural Neural Projection Dynamics Underlying Social Behavior Lisa A. Gunaydin, Logan Grosenick, Joel C. Finkelstein, Isaac V. Kauvar, Lief E. Fenno, Avishek Adhikari, Stephan Lammel, Julie J. Mirzabekov, Raag D. Airan, Kelly A. Zalocusky, Kay M. Tye, Polina Anikeeva, Robert C. Malenka, and Karl Deisseroth; Cell 2014 (link)

4) Grid cells and cortical representation Edvard I. Moser, Yasser Roudi, Menno P. Witter, Clifford Kentros, Tobias Bonhoeffer & May-Britt Moser ; Nature Reviews Neuroscience (link)

  • ¬†I really enjoyed this review. For some silly reason¬†I tend to characterize grid cells as a lower level phenomenon- like simple receptive fields in V1 – I guess because I think of how grid fields could be some sort of fundamental unit used to build up a more complex thing.. ..but of course this is a big mistake on my part. I appreciated¬†the reminder that grid fields are located in what would be considered higher order areas of the cortical hierarchy.

5) Lesions of prefrontal cortex reduce attentional modulation of neuronal responses and synchrony in V4 Georgia G Gregoriou, Andrew F Rossi, Leslie G Ungerleider & Robert Desimone ; Nature Neuroscience 2014 (link)

6) A spike-timing mechanism for action selection Catherine R von Reyn, Patrick Breads, Martin Y Peek, Grace Zhiyu Zheng, W Ryan Williamson, Alyson L Yee, Anthony Leonardo & Gwyneth M Card ; Nature Neuroscience 2014 (link)

  • ūüôā

7) Ongoing Network State Controls the Length of Sleep Spindles via Inhibitory Activity Peter Bartho , Andrea Slezia, Ferenc Matyas, Lejla Faradzs-Zade, Istvan Ulbert, Kenneth D. Harris, and Laszlo Acsady ; Neuron 2014 (link)

8) Closed-Loop Decoder Adaptation Shapes Neural Plasticity for Skillful Neuroprosthetic Control Amy L. Orsborn, Helene G. Moorman, Simon A. Overduin, Maryam M. Shanechi, Dragan F. Dimitrov, and Jose M. Carmena ; Neuron 2014 (link)

9) Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements Guillaume Hennequin, Tim P. Vogels, and Wulfram Gerstner; Neuron 2014 (link)

10) Strategy Change in Vibrissal Active Sensing during Rat Locomotion Kendra Arkley, Robyn A. Grant, Ben Mitchinson, and Tony J. Prescott ; Current Biology 2014 (link)

  • I was fortunate enough to catch some videos from this work at a Barrels meeting in the past. Very neat stuff!

11) Dynamics of Neural Population Responses in Prefrontal Cortex Indicate Changes of Mind on Single Trials Roozbeh Kiani, Christopher J. Cueva, John B. Reppas, and William T. Newsome ; Current Biology 2014 (link)

12) The Hippocampus and Entorhinal Cortex Encode the Path and Euclidean Distances to Goals during Navigation Lorelei R. Howard, Amir Homayoun Javadi, Yichao Yu, Ravi D. Mill, Laura C. Morrison, Rebecca Knight, Michelle M. Loftus, Laura Staskute, and Hugo J. Spiers ; Current Biology 2014 (link)

13) All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins Daniel R Hochbaum, Yongxin Zhao, Samouil L Farhi, Nathan Klapoetke, Christopher A Werley, Vikrant Kapoor, Peng Zou, Joel M Kralj, Dougal Maclaurin, Niklas Smedemark-Margulies, Jessica L Saulnier, Gabriella L Boulting, Christoph Straub, Yong Ku Cho, Michael Melkonian, Gane Ka-Shu Wong, D Jed Harrison, Venkatesh N Murthy, Bernardo L Sabatini, Edward S Boyden, Robert E Campbell & Adam E Cohen ; Nature Methods 2014 (link)

  • Could it be? Don’t play with my heart.

14) Targeting cells with single vectors using multiple-feature Boolean logic Lief E Fenno, Joanna Mattis, Charu Ramakrishnan, Minsuk Hyun, Soo Yeun Lee, Miao He, Jason Tucciarone, Aslihan Selimbeyoglu, Andre Berndt, Logan Grosenick, Kelly A Zalocusky, Hannah Bernstein, Haley Swanson, Chelsey Perry, Ilka Diester, Frederick M Boyce, Caroline E Bass, Rachael Neve, Z Josh Huang & Karl Deisseroth ; Nature Methods 2014 (link)

15) Sensory experience during locomotion promotes recovery of function in adult visual cortex Megumi Kaneko, Michael P Stryker ; eLife 2014 (link)

16) Self-motion improves head direction cell tuning Michael E. Shinder and Jeffrey S. Taube ; J Neurophys 2014 (link)

  • Ok… weird elephant in the room question. I’m sure I’ll write something / comment more on the recent Nobel Prize awards.. but doesn’t it feel a bit¬†like Head Direction cells might have gotten the shaft when it comes to Place Cells/ Grid Cells/ Head Direction cells story? I doubt I am the only one¬†who asked this.

17) The Role of Visual Area V4 in the Discrimination of Partially Occluded Shapes Yoshito Kosai, Yasmine El-Shamayleh, Amber M. Fyall, and Anitha Pasupathy ; J Neuroscience 2014 (link)

18) Closed-loop optical neural stimulation based on a 32-channel low-noise recording system with online spike sorting T K T Nguyen, Z Navratilova, H Cabral, L Wang, G Gielen, F P Battaglia and C Bartic ; J NeuroEng 2014 (link)

19) Effect of High-Frequency Stimulation of the Perforant Path on Previously Acquired Spatial Memory in Rats: Influence of Memory Strength and Reactivation Katherine G. Akers, Derek A. Hamilton ; PLoS One 2014 (link)

20)  Points of Significance: Analysis of variance and blocking Martin Krzywinski & Naomi Altman ; Nature Methods 2014 (link)

21) World View: Uprooting researchers can drive them out of science Russell Garwood ; Nature 2014 (link)