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–inhibition 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)

  • 🙂

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)



Friday Paper Post- posted Sunday June 8th 2014

Plenty of great papers lately; including new tricks with optogenetics. For example, the picture below demonstrates some lovely optogenetic manipulation of behavior.


1) Engineering a memory with LTD and LTP Sadegh Nabavi, Rocky Fox, Christophe D. Proulx, John Y. Lin, Roger Y. Tsien & Roberto Malinow ; Nature 2014 (link)

2) Composition of isolated synaptic boutons reveals the amounts of vesicle trafficking proteins Benjamin G. Wilhelm, Sunit Mandad, Sven Truckenbrodt, Katharina Kröhnert, Christina Schäfer, Burkhard Rammner, Seong Joo Koo, Gala A. Claßen, Michael Krauss, Volker Haucke, Henning Urlaub, Silvio O. Rizzoli ; Science 2014 (link)

3) Sleep promotes branch-specific formation of dendritic spines after learning Guang Yang, Cora Sau Wan Lai, Joseph Cichon, Lei Ma, Wei Li, Wen-Biao Gan ; Science 2014 (link)

4) Two distinct layer-specific dynamics of cortical ensembles during learning of a motor task Yoshito Masamizu, Yasuhiro R Tanaka, Yasuyo H Tanaka, Riichiro Hira, Fuki Ohkubo, Kazuo Kitamura, Yoshikazu Isomura, Takashi Okada & Masanori Matsuzaki ; Nature Neuroscience 2014 (link)

5) Patterns across multiple memories are identified over time Blake A Richards, Frances Xia, Adam Santoro, Jana Husse, Melanie A Woodin, Sheena A Josselyn & Paul W Frankland ; Nature Neuroscience 2014 (link)

6) 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)

7) Sleep and Movement Differentiates Actions of Two Types of Somatostatin-Expressing GABAergic Interneuron in Rat Hippocampus Linda Katona, Damien Lapray, Tim J. Viney, Abderrahim Oulhaj, Zsolt Borhegyi, Benjamin R. Micklem, Thomas Klausberger, and Peter Somogyi ; Neuron 2014 (link)

8) Cell Types, Network Homeostasis, and Pathological Compensation from a Biologically Plausible Ion Channel Expression Model Timothy O’Leary, Alex H. Williams, Alessio Franci, and Eve Marder ; Neuron 2014 (link)

9) Wide-Field Feedback Neurons Dynamically Tune Early Visual Processing John C. Tuthill, Aljoscha Nern, Gerald M. Rubin, and Michael B. Reiser ; Neuron 2014 (link)

10) Multipoint-Emitting Optical Fibers for Spatially Addressable In Vivo Optogenetics Ferruccio Pisanello, Leonardo Sileo, Ian A. Oldenburg, Marco Pisanello, Luigi Martiradonna, John A. Assad, Bernardo L. Sabatini, and Massimo De Vittorio ; Neuron 2014 (link)

11) Hippocampal Representation of Related and Opposing Memories Develop within Distinct, Hierarchically Organized Neural Schemas Sam McKenzie, Andrea J. Frank, Nathaniel R. Kinsky, Blake Porter, Pamela D. Riviere, and Howard Eichenbaum ; Neuron 2014 (link)

12) Binocular Integration in the Mouse Lateral Geniculate Nuclei Michael Howarth, Lauren Walmsley, and Timothy M. Brown ; Current Biology 2014 (link)

13) Neural Pathways for the Detection and Discrimination of Conspecific Song in D. melanogaster Alexander G. Vaughan, Chuan Zhou, Devanand S. Manoli, and Bruce S. Baker  ; Current Biology 2014 (link)

14) Face-selective neurons maintain consistent visual responses across months David B. T. McMahon, Adam P. Jones, Igor V. Bondar, and David A. Leopold ; PNAS 2014 (link)

15) Mouse Visual Neocortex Supports Multiple Stereotyped Patterns of Microcircuit Activity Alexander J. Sadovsky and Jason N. MacLean ; J. Neuroscience 2014 (link)


Friday Paper Post – May 24th 2014 (back from the dead pt. 4)

Alright this is it! I should finally be caught back up with this last list of papers! Whoo Hoo!

1) Crystal structure of the human glucose transporter GLUT1 Dong Deng, Chao Xu, Pengcheng Sun, Jianping Wu, Chuangye Yan, Mingxu Hu & Nieng Yan ; Nature 2014 (link)

2) Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis Etsuo A. Susaki, Kazuki Tainaka, Dimitri Perrin, Fumiaki Kishino, Takehiro Tawara, Tomonobu M. Watanabe, Chihiro Yokoyama, Hirotaka Onoe, Megumi Eguchi, Shun Yamaguchi, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Shimizu, Atsushi Miyawaki, Hideo Yokota, and Hiroki R. Ueda ; Cell 2014 (link)

3) FoxP influences the speed and accuracy of a perceptual decision in Drosophila Shamik DasGupta, Clara Howcroft Ferreira, Gero Miesenböck ; Science 2014 (link)

4) Rapid Hebbian axonal remodeling mediated by visual stimulation Martin Munz, Delphine Gobert, Anne Schohl, Jessie Poquérusse, Kaspar Podgorski, Perry Spratt, Edward S. Ruthazer ; Science 2014 (link)

5) Spatiotemporal receptive fields of barrel cortex revealed by reverse correlation of synaptic input Alejandro Ramirez, Eftychios A Pnevmatikakis, Josh Merel, Liam Paninski, Kenneth D Miller & Randy M Bruno ; Nature Neuroscience 2014 (link)

6) Simultaneous whole- animal 3d imaging of neuronal activity using light-field microscopy Robert Prevedel, Young-Gyu Yoon, Maximilian Hoffmann, Nikita Pak, Gordon Wetzstein, Saul Kato, Tina Schrödel, Ramesh Raskar, Manuel Zimmer, Edward S Boyden & Alipasha Vaziri ; Nature Methods 2014 (link)

  • Aright, so I want to make sure I am clear on where things are now…
  • We have the entire connectome of C. Elegans mapped out..
  • …and now we also have the ability to image every single neuron simultaneously (yes I know it’s calcium imaging….so not every single spike exactly… but pretty close)
  • So now with the full connectome and functional readout we should be able to figure it all out right? I mean it’s that easy right? There is always whining that we need one or the other to truly understand the full story.. but now we’ve got both! No more excuses! I want to know how the C. Elegans brain works already.

7) Parvalbumin-Positive Basket Cells Differentiate among Hippocampal Pyramidal Cells Sang-Hun Lee, Ivan Marchionni, Marianne Bezaire, Csaba Varga, Nathan Danielson, Matthew Lovett-Barron, Attila Losonczy, and Ivan Soltesz ; Neuron 2014 (link)

8) Dendritic Spikes Induce Ripples in Parvalbumin Interneurons during Hippocampal Sharp Waves Balazs Chiovini, Gergely F. Turi, Gergely Katona, Attila Kaszas, Denes Palfi, Pal Maak, Gergely Szalay, Matyas Forian Szabo ́ , Gabor Szabo, Zoltan Szadai,  Szabolcs Kali, and Balazs Rozsa  ; Neuron 2014 (link)

9) New and Distinct Hippocampal Place Codes Are Generated in a New Environment during Septal Inactivation Mark P. Brandon, Julie Koenig, Jill K. Leutgeb, and Stefan Leutgeb  ; Neuron 2014 (link)

  • Are New Place Representations Independent of Theta and Path Integration? Robin Hayman and Neil Burgess  ; Neuron 2014 (link)

10) Visuospatial selective attention in chickens Devarajan Sridharan, Deepa L. Ramamurthy, Jason S. Schwarz, and Eric I. Knudsen ; PNAS 2014 (link)

11) Hippocampal Replay Captures the Unique Topological Structure of a Novel Environment Xiaojing Wu and David J. Foster ; J Neuroscience 2014 (link)

Friday Paper Post – May 24th 2014 (back from the dead pt. 3)

1) Spatially Distributed Local Fields in the Hippocampus Encode Rat Position Gautam Agarwal, Ian H. Stevenson, Antal Berényi, Kenji Mizuseki, György Buzsáki, Friedrich T. Sommer ; Science 2014 (link)

  • I really enjoyed this paper!
  • Also after following a reader’s twitter (who shared the wonderful ferret spiral move above and whose own blog you can read here) I was lucky enough to be lead to this blog post from Bill Skaggs here.
  • What I really like about the blog post is the back and forth in the commentary from Dr. Skaggs and the first author of the Science paper. I wish there was more scientific discussion like this online. It would be kind of cool if every paper had a comments section! Ok…. with the way the internet and comments sections usually turn out….maybe not … but I can dream.

2) Hippocampal Neurogenesis Regulates Forgetting During Adulthood and Infancy Katherine G. Akers, Alonso Martinez-Canabal, Leonardo Restivo, Adelaide P. Yiu, Antonietta De Cristofaro, Hwa-Lin (Liz) Hsiang, Anne L. Wheeler, Axel Guskjolen, Yosuke Niibori, Hirotaka Shoji, Koji Ohira, Blake A. Richards, Tsuyoshi Miyakawa, Sheena A. Josselyn, Paul W. Frankland ; Science 2014 (link)

3) Molecular-Level Functional Magnetic Resonance Imaging of Dopaminergic Signaling Taekwan Lee, Lili X. Cai, Victor S. Lelyveld, Aviad Hai, Alan Jasanoff ; Science 2014 (link)

4) Presynaptic inhibition of spinal sensory feedback ensures smooth movement Andrew J. P. Fink, Katherine R. Croce, Z. Josh Huang, L. F. Abbott, Thomas M. Jessell & Eiman Azim ; Nature 2014 (link)

  • Feedback throttled down for smooth moves Stephen H. Scott & Frederic Crevecoeur ; Nature 2014 (link)

5) Modality-specific thalamocortical inputs instruct the identity of postsynaptic L4 neurons Gabrielle Pouchelon, Fre ́de ́ric Gambino, Camilla Bellone, Ludovic Telley, Ilaria Vitali, Christian Lu ̈scher, Anthony Holtmaat & Denis Jabaudon ; Nature 2014 (link)

6) Purkinje-cell plasticity and cerebellar motor learning are graded by complex-spike duration Yan Yang & Stephen G. Lisberger ; Nature 2014 (link)

7) Emergence of reproducible spatiotemporal activity during motor learning Andrew J. Peters, Simon X. Chen & Takaki Komiyama ; Nature 2014 (link)

8) Anthropogenic electromagnetic noise disrupts magnetic compass orientation in a migratory bird Svenja Engels, Nils-Lasse Schneider, Nele Lefeldt, Christine Maira Hein, Manuela Zapka, Andreas Michalik, Dana Elbers, Achim Kittel, P. J. Hore & Henrik Mouritsen ; Nature 2014 (link)

9) Amygdala interneuron subtypes control fear learning through disinhibition Steffen B. E. Wolff, Jan Gru ̈ndemann, Philip Tovote, Sabine Krabbe, Gilad A. Jacobson, Christian Mu ̈ller, Cyril Herry, Ingrid Ehrlich, Rainer W. Friedrich, Johannes J. Letzkus & Andreas Lu ̈thi ; Nature 2014 (link)

10) Space–time wiring specificity supports direction selectivity in the retina Jinseop S. Kim, Matthew J. Greene, Aleksandar Zlateski, Kisuk Lee, Mark Richardson, Srinivas C. Turaga, Michael Purcaro, Matthew Balkam, Amy Robinson, Bardia F. Behabadi, Michael Campos, Winfried Denk, H. Sebastian Seung & the EyeWirers ; Nature 2014 (link)

  • Notice the final author in this paper is the EyeWire online community.

11) Partitioning neuronal variability Robbe L T Goris, J Anthony Movshon & Eero P Simoncelli ; Nature Neuroscience 2014 (link)

12) Induction of self awareness in dreams through frontal low current stimulation of gamma activity Ursula Voss, Romain Holzmann, Allan Hobson, Walter Paulus, Judith Koppehele-Gossel, Ansgar Klimke & Michael A Nitsche ; Nature Neuroscience 2014 (link)

13) Cortical control of adaptation and sensory relay mode in the thalamus Rebecca A. Mease, Patrik Krieger, and Alexander Groh ; PNAS 2014 (link)

14) Comparative Strength and Dendritic Organization of Thalamocortical and Corticocortical Synapses onto Excitatory Layer 4 Neurons Carl E. Schoonover, Juan-Carlos Tapia, Verena C. Schilling, Verena Wimmer, Richard Blazeski, Wanying Zhang, Carol A. Mason, and Randy M. Bruno ; J Neuroscience 2014 (link)

15) Natural scenes in tactile texture Louise R. Manfredi, Hannes P. Saal, Kyler J. Brown, Mark C. Zielinski, John F. Dammann III, Vicky S. Polashock, and Sliman J. Bensmaia ; J Neurophysiology 2014 (link)

16) The reactivation of somatosensory cortex and behavioral recovery after sensory loss in mature primates Hui-Xin Qi, Jon H. Kaas and Jamie L. Reed ; Frontiers in Systems Neuroscience 2014  (link)

17) Cortico-cortical communication dynamics Per E. Roland, Claus C. Hilgetag and Gustavo Deco  ; Frontiers in Systems Neuroscience 2014  (link)


Friday Paper Post – May 24th 2014 (back from the dead pt. 2)

Still playing catch-up. Papers below!

1) Successful Execution of Working Memory Linked to Synchronized High-Frequency Gamma Oscillations Jun Yamamoto, Junghyup Suh, Daigo Takeuchi, and Susumu Tonegawa ; Cell 2014 (link)

  • This is an exciting paper, but I can’t help but feel like the use of the term “oops”  is really silly. I keep imagining it being read by Betty Boop 🙂
  • OopsExample1

2) Distinct Profiles of Myelin Distribution Along Single Axons of Pyramidal Neurons in the Neocortex Giulio Srubek Tomassy, Daniel R. Berger, Hsu-Hsin Chen, Narayanan Kasthuri, Kenneth J. Hayworth, Alessandro Vercelli, H. Sebastian Seung, Jeff W. Lichtman, Paola Arlotta ; Science 2014 (link)

  • I like this paper because I think it is a neat example of the type of information electron microscopy reconstructions of the brain can provide.

3) High-fidelity optical reporting of neuronal electrical activity with an ultrafast fluorescent voltage sensor François St-Pierre, Jesse D Marshall, Ying Yang, Yiyang Gong, Mark J Schnitzer & Michael Z Lin ; Nature Neuroscience 2014 (link)

  • If I’ve said it once I’ve said it a thousand times: the creation of a good genetically encoded voltage sensitive protein indicator would be HUGE.

4) Volitional modulation of optically recorded calcium signals during neuroprosthetic learning Kelly B Clancy, Aaron C Koralek, Rui M Costa, Daniel E Feldman & Jose M Carmena ; Nature Neuroscience 2014 (link)

5) More than a rhythm of life: breathing as a binder of orofacial sensation David Kleinfeld, Martin Deschênes, Fan Wang & Jeffrey D Moore ; Nature Neuroscience 2014 (link)

6) Population code in mouse V1 facilitates readout of natural scenes through increased sparseness Emmanouil Froudarakis, Philipp Berens, Alexander S Ecker, R James Cotton, Fabian H Sinz, Dimitri Yatsenko, Peter Saggau, Matthias Bethge & Andreas S Tolias ; Nature Neuroscience 2014 (link)

7) Executive control processes underlying multi-item working memory Antonio H Lara & Jonathan D Wallis ; Nature Neuroscience 2014 (link)

8) Scaling down of balanced excitation and inhibition by active behavioral states in auditory cortex Mu Zhou, Feixue Liang, Xiaorui R Xiong, Lu Li, Haifu Li, Zhongju Xiao, Huizhong W Tao & Li I Zhang ; Nature Neuroscience 2014 (link)

9) Chronic, wireless recordings of large-scale brain activity in freely moving rhesus monkeys David A Schwarz, Mikhail A Lebedev, Timothy L Hanson, Dragan F Dimitrov, Gary Lehew, Jim Meloy, Sankaranarayani Rajangam, Vivek Subramanian, Peter J Ifft, Zheng Li, Arjun Ramakrishnan, Andrew Tate, Katie Z Zhuang & Miguel A L Nicolelis ; Nature Methods 2014 (link)

  • I believe I have also professed my huge fandom of Miguel Nicolelis and his work. This paper did not disappoint 😀

10) Learning Precisely Timed Spikes Raoul-Martin Memmesheimer, Ran Rubin, Bence P. O ̈ lveczky, and Haim Sompolinsky ; Neuron 2014 (link)

11) Flying Drosophila stabilize their vision-based velocity controller by sensing wind with their antennae Sawyer Buckminster Fuller, Andrew D. Straw, Martin Y. Peek, Richard M. Murray, and Michael H. Dickinson ; PNAS 2014 (link)

12) Symbol addition by monkeys provides evidence for normalized quantity coding Margaret S. Livingstone, Warren W. Pettine, Krishna Srihasam, Brandon Moore, Istvan A. Morocz, and Daeyeol Lee ; PNAS 2014 (link)

13) Out-of-body–induced hippocampal amnesia Loretxu Bergouignan, Lars Nyber, and H. Henrik Ehrsson ; PNAS 2014 (link)

14) Restoring sensorimotor function through intracortical interfaces: progress and looming challenges Sliman J. Bensmaia and Lee Miller ; Nature Reviews Neuroscience 2014 (link)

15) Subnanometre resolution in three-dimensional magnetic resonance imaging of individual dark spins M. S. Grinolds, M. Warner, K. De Greve, Y. Dovzhenko, L. Thiel, R. L. Walsworth, S. Hong, P. Maletinsky and A. Yacoby; Nature Nanotechnology 2014 (link)

16) Optogenetic inhibition of neurons by internal light production Benjamin B. Land, Catherine E. Brayton, Kara E. Furman, Zoe LaPalombara and Ralph J. DiLeone ; Frontiers In Behavioral Neuroscience 2014 (link)

Shout out to Martin and Brandon on the papers! Congrats!

Friday Paper Post- May 18th 2014 (back from the dead pt. 1)

Unfortunately there were no posts this April; however, much to my relief, the neuroscience community was very considerate towards my blogging schedule and decided to postpone all publications until I could find time to blog about them!!

…wait…. no that’s not true at all…

Alright.. let’s do this!

1) Neural Mechanisms of Object-Based Attention Daniel Baldauf and Robert Desimone ; Science 2014 (link)

2) Soft Microfluidic Assemblies of Sensors, Circuits, and Radios for the Skin Sheng Xu, Yihui Zhang, Lin Jia, Kyle E. Mathewson, Kyung-In Jang, Jeonghyun Kim, Haoran Fu, Xian Huang, Pranav Chava, Renhan Wang, Sanat Bhole, Lizhe Wang, Yoon Joo Na, Yue Guan, Matthew Flavin, Zheshen Han, Yonggang Huang, John A. Rogers  ; Science 2014 (link)

3) Flies Evade Looming Targets by Executing Rapid Visually Directed Banked Turns Florian T. Muijres, Michael J. Elzinga, Johan M. Melis, Michael H. Dickinson ; Science 2014 (link)

4) Conversion of Channelrhodopsin into a Light-Gated Chloride Channel Jonas Wietek, J. Simon Wiegert, Nona Adeishvili, Franziska Schneider, Hiroshi Watanabe, Satoshi P. Tsunoda, Arend Vogt, Marcus Elstner, Thomas G. Oertner, Peter Hegemann ; Science 2014 (link)

5) Structure-Guided Transformation of Channelrhodopsin into a Light-Activated Chloride Channel Andre Berndt, Soo Yeun Lee, Charu Ramakrishnan, Karl Deisseroth ; Science 2014 (link)

  • Silencing Neurons with Light Shigehiko Hayashi ; Science 2014 (link)

6) Neuronal Control of Drosophila Walking Direction Salil S. Bidaye, Christian Machacek, Yang Wu, Barry J. Dickson ; Science 2014 (link)

7) A mesoscale connectome of the mouse brain Seung Wook Oh, Julie A. Harris, Lydia Ng, Brent Winslow, Nicholas Cain, Stefan Mihalas, Quanxin Wang, Chris Lau, Leonard Kuan, Alex M. Henry, Marty T. Mortrud, Benjamin Ouellette, Thuc Nghi Nguyen, Staci A. Sorensen, Clifford R. Slaughterbeck, Wayne Wakeman, Yang Li1, David Feng, Anh Ho, Eric Nicholas, Karla E. Hirokawa, Phillip Bohn, Kevin M. Joines, Hanchuan Peng, Michael J. Hawrylycz, John W. Phillips, John G. Hohmann, Paul Wohnoutka, Charles R. Gerfen, Christof Koch, Amy Bernard, Chinh Dang, Allan R. Jones & Hongkui Zeng ; Nature 2014 (link)

8) Transcriptional landscape of the prenatal human brain Jeremy A. Miller, Song-Lin Ding, Susan M. Sunkin, Kimberly A. Smith, Lydia Ng, Aaron Szafer, Amanda Ebbert, Zackery L. Riley, Joshua J. Royall, Kaylynn Aiona, James M. Arnold, Crissa Bennet, Darren Bertagnolli, Krissy Brouner, Stephanie Butler, Shiella Caldejon, Anita Carey, Christine Cuhaciyan, Rachel A. Dalley, Nick Dee, Tim A. Dolbeare, Benjamin A. C. Facer, David Feng, Tim P. Fliss, Garrett Gee, Jeff Goldy, Lindsey Gourley, Benjamin W. Gregor, Guangyu Gu, Robert E. Howard, Jayson M. Jochim, Chihchau L. Kuan, Christopher Lau, Chang-Kyu Lee, Felix Lee, Tracy A. Lemon, Phil Lesnar, Bergen McMurray, Naveed Mastan, Nerick Mosqueda, Theresa Naluai-Cecchini, Nhan-Kiet Ngo, Julie Nyhus, Aaron Oldre, Eric Olson, Jody Parente, Patrick D. Parker, Sheana E. Parry, Allison Stevens, Mihovil Pletikos, Melissa Reding, Kate Roll, David Sandman, Melaine Sarreal, Sheila Shapouri, Nadiya V. Shapovalova, Elaine H. Shen, Nathan Sjoquist, Clifford R. Slaughterbeck, Michael Smith, Andy J. Sodt, Derric Williams, Lilla Zo ̈llei, Bruce Fischl, Mark B. Gerstein, Daniel H. Geschwind, Ian A. Glass, Michael J. Hawrylycz, Robert F. Hevner, Hao Huang, Allan R. Jones, James A. Knowles, Pat Levitt, John W. Phillips, Nenad Sˇestan, Paul Wohnoutka, Chinh Dang, Amy Bernard, John G. Hohmann & Ed S. Lein ; Nature 2014 (link)

  • The two papers above represent a milestone for what will hopefully be the first of many publications from the Allen Brain Institute.

9) Epidermal Merkel cells are mechanosensory cells that tune mammalian touch receptors Srdjan Maksimovic, Masashi Nakatani, Yoshichika Baba, Aislyn M. Nelson, Kara L. Marshall, Scott A. Wellnitz, Pervez Firozi, Seung-Hyun Woo, Sanjeev Ranade, Ardem Patapoutian & Ellen A. Lumpkin  ; Nature 2014 (link)

10) Piezo2 is required for Merkel-cell mechanotransduction Seung-Hyun Woo, Sanjeev Ranade, Andy D. Weyer, Adrienne E. Dubin, Yoshichika Baba, Zhaozhu Qiu, Matt Petrus, Takashi Miyamoto, Kritika Reddy, Ellen A. Lumpkin, Cheryl L. Stucky & Ardem Patapoutian  ; Nature 2014 (link)

11) BRIEF COMMUNICATIONS ARISING Interneuron subtypes and orientation tuning ARISING FROM B. V. Atallah, W. Bruns, M. Carandini & M. Scanziani Neuron 73, 159–170 (2012); N. R. Wilson, C. A. Runyan, F. L. Wang & M. Sur Nature 488, 343–348 (2012); S.-H. Lee et al. Nature 488, 379–383 (2012) Seung-Hee Lee, Alex C. Kwan & Yang Dan; Nature 2014 (link)

  • Atallah et al. reply Bassam V. Atallah, Massimo Scanziani & Matteo Carandini ; Nature 2014 (link)
  • El-Boustani et al. reply Sami El-Boustani, Nathan R. Wilson, Caroline A. Runyan & Mriganka Sur ; Nature 2014 (link)
  • I presented the three papers mentioned at the top of this in a lab meeting once and was delighted by the fact that they each reported slightly different results to a similar question about the role of interneuron subtypes in rodent visual cortex. It’s really cool to get to read these follow up communications!

12) Coordination of entorhinal–hippocampal ensemble activity during associative learning Kei M. Igarashi, Li Lu, Laura L. Colgin, May-Britt Moser & Edvard I. Moser  ; Nature 2014 (link)

13) Universal computing by DNA origami robots in a living animal Yaniv Amir, Eldad Ben-Ishay, Daniel Levner, Shmulik Ittah, Almogit Abu-Horowitz and Ido Bachelet ; Nature Nanotechnology 2014 (link)

  • I could not possibly resist including this paper in the list. I mean just read the title!! WE ARE LIVING IN THE FUTURE ! ! ! 😀

14) Parvalbumin interneurons provide grid cell–driven recurrent inhibition in the medial entorhinal cortex Christina Buetfering, Kevin Allen & Hannah Monyer ; Nature Neuroscience 2014 (link)

15) Contributions and challenges for network models in cognitive neuroscience Olaf Sporns  ; Nature Neuroscience 2014 (link)

16) Rapid adaptive optical recovery of optimal resolution over large volumes Kai Wang, Daniel E Milkie, Ankur Saxena, Peter Engerer, Thomas Misgeld, Marianne E Bronner, Jeff Mumm & Eric Betzig ; Nature Methods 2014 (link)

17) The Extrageniculate Visual Pathway Generates Distinct Response Properties in the Higher Visual Areas of Mice Manavu Tohmi, Reiko Meguro, Hiroaki Tsukano, Ryuichi Hishida, and Katsuei Shibuki ; Current Biologgy 2014 (link)

18) Neural Mechanisms of Self-Location C. Barry and N. Burgess  ; Current Biologgy 2014 (link)

19) Slow and Fast Gamma Rhythms Coordinate Different Spatial Coding Modes in Hippocampal Place Cells Kevin Wood Bieri, Katelyn N. Bobbitt, and Laura Lee Colgin ; Neuron 2014 (link)

20) State Dependence of Noise Correlations in Macaque Primary Visual Cortex Alexander S. Ecker, Philipp Berens, R. James Cotton, Manivannan Subramaniyan, George H. Denfield, Cathryn R. Cadwell, Stelios M. Smirnakis, Matthias Bethge, and Andreas S. Tolias ; Neuron 2014 (link)

  • Correlated activity in the brain is a hot topic and in 2010 when Science published Ecker et al. and Renart et al.,  there was a decent the splash in the neuroscience community. This paper above aims to be a follow for some of this work.

21) Learning-Induced Plasticity Regulates Hippocampal Sharp Wave-Ripple Drive Gabrielle Girardeau, Anne Cei, and Michae ̈l Zugaro ; J Neuroscience 2014 (link)

22) Slow-Wave Sleep-Imposed Replay Modulates Both Strength and Precision of Memory Dylan C. Barnes and Donald A. Wilson ; J Neuroscience 2014 (link)

23) Auditory Thalamus and Auditory Cortex Are Equally Modulated by Context during Flexible Categorization of Sounds Santiago Jaramillo, Katharine Borges, and Anthony M. Zador ; J Neuroscience 2014 (link)

24) Optogenetic Assessment of Horizontal Interactions in Primary Visual Cortex Xiaoying Huang, Yishai M. Elyada, William H. Bosking, Theo Walker, and David Fitzpatrick ; J Neuroscience 2014 (link)

  • I was a really big fan of this work when I first caught it at SFN meetings in the past. I was particularly drawn in by the use of optogenetics, intrinsic signal optical imaging, and electrophysiology. Now I am super excited to read the results!

25) Microcircuitry of Agranular Frontal Cortex: Testing the Generality of the Canonical Cortical Microcircuit David C. Godlove, Alexander Maier, Geoffrey F. Woodman, and Jeffrey D. Schall ; J Neuroscience 2014 (link)

26) Microvibrissae-Based Texture Discrimination Praveen Kuruppath, Erez Gugig, and Rony Azouz ; J Neuroscience 2014 (link)

27) Behavioral Oscillations in Attention: Rhythmic α Pulses Mediated through θ Band Kun Song, Ming Meng, Lin Chen, Ke Zhou, and Huan Luo ; J Neuroscience 2014 (link)

28) A Hybrid Oscillatory Interference/Continuous Attractor Network Model of Grid Cell Firing Daniel Bush and Neil Burgess ; J Neuroscience 2014 (link)

29) Operant Conditioning of Synaptic and Spiking Activity Patterns in Single Hippocampal Neurons Daisuke Ishikawa, Nobuyoshi Matsumoto, Tetsuya Sakaguchi, Norio Matsuki, and Yuji Ikegaya ; J Neuroscience 2014 (link)


alright … more papers to follow…


Friday Paper Post – Posted Monday March 31st 2014

I had the opportunity to hear Josh Vogelstein (the first author of paper #1 below) give an awesome talk about big data and neuroscience at a meeting a few years ago and I really enjoyed it! Josh works in the Department of Statistical Science at Duke University and serves as a pleasant reminder of how important statistics are for science in general and especially for neuroscience moving forward. #20 and the paired blog post follow the same theme of statistics in neuroscience.

#3 talks about some problems in big data and the old computer science saying, “Garbage in, garbage out“. It’s kind of interesting to think about how this applies to neuroscience, if at all… but I’ll save my random thoughts for myself.

Paper below!

1) Discovery of Brainwide Neural- Behavioral Maps via Multiscale Unsupervised Structure Learning Joshua T. Vogelstein, Youngser Park, Tomoko Ohyama,  Rex Kerr, James W. Truman, Carey E. Priebe,  Marta Zlatic ; Science 2014 (link)

2) Humans Can Discriminate More than 1 Trillion Olfactory Stimuli C. Bushdid, M. O. Magnasco, L. B. Vosshall, A. Keller ; Science 2014 (link)

3) The Parable of Google Flu: Traps in Big Data Analysis David Lazer, Ryan Kennedy, Gary King, Alessandro Vespignani ; Science 2014 (link)

4) Optical Broadband Angular Selectivity Yichen Shen, Dexin Ye, Ivan Celanovic, Steven G. Johnson, John D. Joannopoulos, Marin Soljačić ; Science 2014 (link)

5) Visual space is compressed in prefrontal cortex before eye movements Marc Zirnsak, Nicholas A. Steinmetz, Behrad Noudoost, Kitty Z. Xu & Tirin Moore ; Nature 2014 (link)

6) Sensory stimulation shifts visual cortex from synchronous to asynchronous states Andrew Y. Y. Tan, Yuzhi Chen, Benjamin Scholl, Eyal Seidemann & Nicholas J. Priebe ; Nature 2014 (link)

7)  The Molecular and Systems Biology of Memory Eric R. Kandel, Yadin Dudai, and Mark R. Mayford ; Cell 2014 (link)

8) A Framework for Studying Emotions across Species David J. Anderson and Ralph Adolphs ; Cell 2014 (link)

9) Memory loss in a nonnavigational spatial task after hippocampal inactivation in monkeys Patrick A. Forcelli, Guillermo Palchik, Taylor Leath, Jacqueline T. DesJardin, Karen Gale, and Ludise Malkova ; PNAS 2014 (link)

10) Mossy fiber-evoked subthreshold responses induce timing-dependent plasticity at hippocampal CA3 recurrent synapses Federico Brandalise and Urs Gerber ; PNAS 2014 (link)

11) Identification of ocular dominance domains in New World owl monkeys by immediate-early gene expression Toru Takahataa, Masanobu Miyashitab, Shigeru Tanakac, and Jon H. Kaas ; PNAS 2014 (link)

12) Whole-Brain Activity Maps Reveal Stereotyped, Distributed Networks for Visuomotor Behavior Ruben Portugues, Claudia E. Feierstein, Florian Engert, and Michael B. Orger ; Neuron 2014 (link)

13) Functional Architecture of an Optic Flow-Responsive Area that Drives Horizontal Eye Movements in Zebrafish Fumi Kubo, Bastian Hablitzel, Marco Dal Maschio, Wolfgang Driever, Herwig Baier, and Aristides B. Arrenberg ; Neuron 2014 (link)

14) Learned spatiotemporal sequence recognition and prediction in primary visual cortex Jeffrey P Gavornik & Mark F Bear ; Nature Neuroscience 2014 (link)

15) Unbalanced excitability underlies offline reactivation of behaviorally activated neurons Mika Mizunuma, Hiroaki Norimoto, Kentaro Tao , Takahiro Egawa , Kenjiro Hanaoka , Tetsuya Sakaguchi , Hiroyuki Hioki, Takeshi Kaneko, Shun Yamaguchi, Tetsuo Nagano, Norio Matsuki & Yuji Ikegaya ; Nature Neuroscience 2014 (link)

16) Two types of asynchronous activity in networks of excitatory and inhibitory spiking neurons Srdjan Ostojic ; Nature Neuroscience 2014 (link)

  • Useful dynamic regimes emerge in recurrent networks Vishwa Goudar & Dean V Buonomano ; Nature Neuroscience 2014 (link)

17) Object-based attention involves the sequential activation of feature-specific cortical modules Mircea A Schoenfeld, Jens-Max Hopf , Christian Merkel, Hans-Jochen Heinze & Steven A Hillyard Nature Neuroscience 2014 (link)

18) Spine neck plasticity regulates compartmentalization of synapses Jan Tønnesen, Gergely Katona, Balázs Rózsa & U Valentin Nägerl ; Nature Neuroscience 2014 (link)

19) Designer receptors show role for ventral pallidum input to ventral tegmental area in cocaine seeking Stephen V Mahler, Elena M Vazey, Jacob T Beckley, Colby R Keistler, Ellen M McGlinchey, Jennifer Kaufling, Steven P Wilson, Karl Deisseroth, John J Woodward & Gary Aston-Jones ; Nature Neuroscience 2014 (link)

20) A solution to dependency: using multilevel analysis to accommodate nested data Emmeke Aarts, Matthijs Verhage, Jesse V Veenvliet, Conor V Dolan & Sophie van der Sluis ; Nature Neuroscience 2014 (link)

  • Statistical Flaw Punctuates Brain Research in Elite Journals  Gary Stix ; Scientific American Blog: Talking Back 2014 (link)

21) Attentive scanning behavior drives one-trial potentiation of hippocampal place fields Joseph D Monaco, Geeta Rao, Eric D Roth & James J Knierim Nature Neuroscience 2014 (link)

22) Reversed theta sequences of hippocampal cell assemblies during backward travel Anne Cei, Gabrielle Girardeau, Céline Drieu, Karim El Kanbi & Michaël Zugaro ; Nature Neuroscience 2014 (link)

  • This paper is just plain awesome. This post was easily my favorite from SFN last year and you can see the great set up they used in panel A of their figure 1 below. So excited to see the movie now!
  • rat_train

23) Serial dependence in visual perception Jason Fischer & David Whitney ; Nature Neuroscience 2014 (link)

24) Long term functional plasticity of sensory inputs mediated by olfactory learning Nixon M Abraham, Roberto Vincis, Samuel Lagier, Ivan Rodriguez, Alan Carleton ; eLife 2014 (link)

25) CA1 cell activity sequences emerge after reorganization of network correlation structure during associative learning Mehrab N Modi, Ashesh K Dhawale, Upinder S Bhalla ; eLife 2014 (link)

  • Hippocampal neurons wait their turn Yuan Gao and Ian Davison ; eLife 2014 (link)

26) Behavioral flexibility is increased by optogenetic inhibition of neurons in the nucleus accumbens shell during specific time segments Luca Aquili, Andrew W. Liu, Mayumi Shindou, Tomomi Shindou, and Jeffery R. Wickens ; Learning and Memory 2014 (link)

27) Multisensory Response Modulation in the Superficial Layers of the Superior Colliculus Dipanwita Ghose, Alexander Maier, Aaron Nidiffer, and Mark T. Wallace ; J Neuroscience 2014 (link)

28) Cortical Neuron Response Properties Are Related to Lesion Extent and Behavioral Recovery after Sensory Loss from Spinal Cord Injury in Monkeys Hui-Xin Qi, Jamie L. Reed, Omar A. Gharbawie, Mark J. Burish, and Jon H. Kaas ; J Neuroscience 2014 (link)

29) Dendritic Inhibition Provided by Interneuron-Specific Cells Controls the Firing Rate and Timing of the Hippocampal Feedback Inhibitory Circuitry Leonid Tyan, Simon Chamberland, Elise Magnin, Olivier Camire ́, Ruggiero Francavilla, Linda Suzanne David, Karl Deisseroth, and Lisa Topolnik ; J Neuroscience 2014 (link)

30) Differential Coding of Conspecific Vocalizations in the Ventral Auditory Cortical Stream Makoto Fukushima, Richard C. Saunders, David A. Leopold, Mortimer Mishkin, and Bruno B. Averbeck ; J Neuroscience 2014 (link)

31) A Unified Mathematical Framework for Coding Time, Space, and Sequences in the Hippocampal Region Marc W. Howard, Christopher J. MacDonald, Zoran Tiganj, Karthik H. Shankar, Qian Du, Michael E. Hasselmo, and Howard Eichenbaum ; J Neuroscience 2014 (link)