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)



Friday Paper Post – March 14th 2014

Is winter over yet?

I wanted to share a couple non-paper links I found interesting recently. The first few are depressing…

Here is an interview with Sydner Brenner by Elizabeth Dzeng that turns into a sharp commentary on the state of science.

Scientific funding is in a scary place right now. You can read some of the details at this post titled: The Impact of the sequester: 1,000 fewer funded investigators by Jeremy Berg.

Finally check out this blog post here by Lenny Teytelman, which gives a more personal account of how tough things are. I think it is well worth the read.

So… anyway… these are all sad / scary / depressing / grim things…. but I am very happy to link to this last post here from the PubPeer blog! I think I have mentioned before that I have strong feelings about the state of the scientific publishing system (broken, slow, costly, and kind of embarrassing considering there is this thing now called the internet.. maybe you’ve heard of it?). So I think this blog post is really an exciting step forward! There is hope for the future!!!

Alright.. enough writing.. papers below!

1) A Cortical Circuit for Gain Control by Behavioral State Yu Fu, Jason M. Tucciarone, J. Sebastian Espinosa, Nengyin Sheng, Daniel P. Darcy, Roger A. Nicoll, Z. Josh Huang, and Michael P. Stryker ; Cell 2014 (link)

  • How can I not post this great graphical abstract 🙂
  • PIIS0092867414001445.fx1.lrg
  • Visual Circuits Get the VIP Treatment Ashley M. Wilson and Lindsey L. Glickfeld ; Cell 2014 (link)

2) Dynamic sensory cues shape song structure in Drosophila Philip Coen, Jan Clemens, Andrew J. Weinstein, Diego A. Pacheco, Yi Deng & Mala Murthy ; Nature 2014 (link)

3) Computational neuroscience: beyond the local circuit Haim Sompolinsky ; Current Opinion in Neurobiology 2014 (link)

4) Perspective: The receptive field is dead. Long live the receptive field? Adrienne Fairhall ; Current Opinion in Neurobiology 2014 (link)

5) Coding of Shape Features in the Macaque Anterior Intraparietal Area Maria C. Romero, Pierpaolo Pani, and Peter Janssen ; J Neuroscience 2014 (link)

6) Brain State Effects on Layer 4 of the Awake Visual Cortex Jun Zhuang (庄骏), Yulia Bereshpolova, Carl R. Stoelzel, Joseph M. Huff, Xiaojuan Hei (黑晓娟), Jose-Manuel Alonso, and Harvey A. Swadlow ; J Neuroscience 2014 (link)

7) Excitatory Synaptic Inputs to Mouse On-Off Direction- Selective Retinal Ganglion Cells Lack Direction Tuning Silvia J.H. Park, In-Jung Kim, Loren L. Looger, Jonathan B. Demb, and Bart G. Borghuis ; J Neuroscience 2014 (link)

8) Identification of a Pathway from the Retina to Koniocellular Layer K1 in the Lateral Geniculate Nucleus of Marmoset Kumiko A. Percival, Amane Koizumi, Rania A. Masri, Peter Buzas, Paul R. Martin, and Ulrike Grunert ; J Neuroscience 2014 (link)

9) Lack of Respiratory Coupling with Neocortical and Hippocampal Slow Oscillations Jeremy Viczko, Arjun V. Sharma, Silvia Pagliardini, Trish Wolansky, and Clayton T. Dickson ; J Neuroscience 2014 (link)

10) Effects of muscimol inactivations of functional domains in motor, premotor, and posterior parietal cortex on complex movements evoked by electrical stimulation Iwona Stepniewska, Omar A. Gharbawie, Mark J. Burish, and Jon H. Kaas ; J Neurophys 2014 (link)

11) Large-scale, high-density (up to 512 channels) recording of local circuits in behaving animals Antal Berényi, Zoltán Somogyvári, Anett J. Nagy, Lisa Roux, John D. Long, Shigeyoshi Fujisawa, Eran Stark, Anthony Leonardo, Timothy D. Harris, and György Buzsáki ; J Neurophys 2014 (link)

12) Grid Cell Spatial Tuning Reduced Following Systemic Muscarinic Receptor Blockade Ehren L. Newman, Jason R. Climer, and Michael E. Hasselmo ; Hippocampus 2014 (link)

13) Simultaneous imaging of neural activity in three dimensions Sean Quirin, Jesse Jackson, Darcy S Peterka and Rafael Yuste ; Frontiers in Neural Circuits 2014 (link)


Friday Paper Post – March 7th 2014

Hopefully bouncing back from a rough start to the blogging schedule in 2014.

Papers below!

1) Neurogenesis in the Striatum of the Adult Human Brain Aurelie Ernst, Kanar Alkass, Samuel Bernard, Mehran Salehpour, Shira Perl, John Tisdale, Goran Possnert, Henrik Druid, and Jonas Frisen ; Cell 2014 (link)

  • more neurons! Woo hoo!

2) Neural Networks of the Mouse Neocortex Brian Zingg, Houri Hintiryan, Lin Gou, Monica Y. Song, Maxwell Bay, Michael S. Bienkowski, Nicholas N. Foster, Seita Yamashita, Ian Bowman, Arthur W. Toga, and Hong-Wei Dong ; Cell 2014 (link)

3) The hippocampal CA2 region is essential for social memory Frederick L. Hitti & Steven A. Siegelbaum ; Nature 2014 (link)

4) A dedicated circuit links direction-selective retinal ganglion cells to the primary visual cortex Alberto Cruz-Martın, Rana N. El-Danaf, Fumitaka Osakada, Balaji Sriram, Onkar S. Dhande, Phong L. Nguyen, Edward M. Callaway, Anirvan Ghosh & Andrew D. Huberman ; Nature 2014 (link)

  • This paper is super awesome! A very cool discovery.

5) Dendritic Inhibition in the Hippocampus Supports Fear Learning Matthew Lovett-Barron, Patrick Kaifosh, Mazen A. Kheirbek, Nathan Danielson, Jeffrey D. Zaremba, Thomas R. Reardon, Gergely F. Turi, René Hen, Boris V. Zemelman, Attila Losonczy ; Science 2014 (link)

6) Action Monitoring and Medial Frontal Cortex: Leading Role of Supplementary Motor Area Francesca Bonini, Boris Burle, Catherine Liégeois-Chauvel, Jean Régis, Patrick Chauvel, Franck Vidal ; Science 2014 (link)

7) Highly Multiplexed Subcellular RNA Sequencing in Situ Je Hyuk Lee,Evan R. Daugharthy, Jonathan Scheiman, Reza Kalhor, Joyce L. Yang, Thomas C. Ferrante, Richard Terry, Sauveur S. F. Jeanty, Chao Li, Ryoji Amamoto, Derek T. Peters, Brian M. Turczyk, Adam H. Marblestone, Samuel A. Inverso, Amy Bernard, Prashant Mali, Xavier Rios, John Aach, George M. Church ; Science 2014 (link)

  • This is a pretty big deal 😛

8) A temporal basis for predicting the sensory consequences of motor commands in an electric fish Ann Kennedy, Greg Wayne, Patrick Kaifosh, Karina Alviña, L F Abbott & Nathaniel B Sawtell ; Nature Neuroscience 2014 (link)

9) Broadly tuned and respiration-independent inhibition in the olfactory bulb of awake mice Brittany N Cazakoff, Billy Y B Lau, Kerensa L Crump, Heike S Demmer & Stephen D Shea ; Nature Neuroscience 2014 (link)

10) Stimulus repetition modulates gamma-band synchronization in primate visual cortex Nicolas M. Bruneta, Conrado A. Bosman, Martin Vinck, Mark Roberts, Robert Oostenveld, Robert Desimone, Peter De Weerd, and Pascal Fries ; PNAS 2014 (link)

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

12) NMDA Receptor-Dependent Multidendrite Ca2+ Spikes Required for Hippocampal Burst Firing In Vivo Christine Grienberger, Xiaowei Chen, and Arthur Konnerth ; Neuron 2014 (link)

13) Layer-Specific GABAergic Control of Distinct Gamma Oscillations in the CA1 Hippocampus Balint Lasztoczi and Thomas Klausberger ; Neuron 2014 (link)

14) Hippocampal Activity Patterns Carry Information about Objects in Temporal Context Liang-Tien Hsieh, Matthias J. Gruber, Lucas J. Jenkins, and Charan Ranganath ; Neuron 2014 (link)

15) Similarity Breeds Proximity: Pattern Similarity within and across Contexts Is Related to Later Mnemonic Judgments of Temporal Proximity Youssef Ezzyat and Lila Davach ; Neuron 2014 (link)

16) Retinal Input Directs the Recruitment of Inhibitory Interneurons into Thalamic Visual Circuits Bruno Golding, Gabrielle Pouchelon, Camilla Bellone, Sahana Murthy, Ariel A. Di Nardo, Subashika Govindan, Masahuro Ogawa, Tomomi Shimogori,Christian Luscher, Alexandre Dayer, and Denis Jabaudon ; Neuron 2014 (link)

17) Representation of Geometric Borders in the Developing Rat Tale L. Bjerknes, Edvard I. Moser, and May-Britt Moser ; Neuron 2014 (link)

18) Structured Connectivity in Cerebellar Inhibitory Networks Sarah Rieubland, Arnd Roth, and Michael Hausser ; Neuron 2014 (link)

19) Corticostriatal Output Gating during Selection from Working Memory Christopher H. Chatham, Michael J. Frank, and David Badre ; Neuron 2014 (link)

20) Statistical Wiring of Thalamic Receptive Fields Optimizes Spatial Sampling of the Retinal Image Luis M. Martinez, Manuel Molano-Mazon,Xin Wang, Friedrich T. Sommer, and Judith A. Hirsch ; Neuron 2014 (link)

21) The Adaptive Trade-Off between Detection and Discrimination in Cortical Representations and Behavior Douglas R. Ollerenshaw, He J.V. Zheng, Daniel C. Millard, Qi Wang, Garrett B. Stanley ; Neuron 2014 (link)

22) Algorithms of whisker-mediated touch perception Miguel Maravall and Mathew E Diamond ; Current Opinion in Neurobiology 2014 (link)

23) Selective Activation of Cholinergic Basal Forebrain Neurons Induces Immediate Sleep-wake Transitions Yong Han, Yu-feng Shi, Wang Xi, Rui Zhou,1 Zhi-bing Tan, Hao Wang, Xiao-ming Li, Zhong Chen, Guoping Feng, Minmin Luo, Zhi-li Huang, Shumin Duan, and Yan-qin Yu ; Current Biology 2014 (link)

24) The log-dynamic brain: how skewed distributions affect network operations György Buzsáki and Kenji Mizuseki ; Nature Reviews Neuroscience 2014 (link)

25) Virally mediated optogenetic excitation and inhibition of pain in freely moving nontransgenic mice Shrivats Mohan Iyer, Kate L Montgomery, Chris Towne, Soo Yeun Lee, Charu Ramakrishnan, Karl Deisseroth & Scott L Delp ; Nature Biotechnology 2014 (link)

26) Procedures for Behavioral Experiments in Head-Fixed Mice Zengcai V. Guo , S. Andrew Hires , Nuo Li , Daniel H. O’Connor , Takaki Komiyama , Eran Ophir ,Daniel Huber , Claudia Bonardi , Karin Morandell , Diego Gutnisky , Simon Peron , Ning-long Xu , James Cox , Karel Svoboda ; PLoS ONE 2014 (link)

  • This is a fantastic paper and an extremely valuable resource as the neuroscience community continues to shift towards taking advantage of the rich set of genetic tools available in the mouse model.

27) RIVETS: A Mechanical System for In Vivo and In Vitro Electrophysiology and Imaging Jason E. Osborne, Joshua T. Dudman  ; PLoS ONE 2014 (link)

28) Encoding of event timing in the phase of neural oscillations Anne Kösem, Alexandre Gramfort, Virginie van Wassenhove ; NeuroImage 2014 (link)

29) The Hippocampal CA2 Ensemble Is Sensitive to Contextual Change Marie E. Wintzer, Roman Boehringer, Denis Polygalov, and Thomas J. McHugh ; J Neuroscience 2014 (link)

30) A Map of LTP-Related Synaptic Changes in Dorsal Hippocampus Following Unsupervised Learning Conor D. Cox, Christopher S. Rex, Linda C. Palmer, Alex H. Babayan, Danielle T. Pham, Samantha D. Corwin, Brian H. Trieu, Christine M. Gall, and Gary Lynch ; J Neuroscience 2014 (link)

31) Extracellular Calcium Controls the Expression of Two Different Forms of Ripple-Like Hippocampal Oscillations Paloma Aivar, Manuel Valero, Elisa Bellistri, and Liset Menendez de la Prida ; J Neuroscience 2014 (link)

32) Differential Entrainment and Learning-Related Dynamics of Spike and Local Field Potential Activity in the Sensorimotor and Associative Striatum Catherine A. Thorn and Ann M. Graybiel ; J Neuroscience 2014 (link)

33) Spatial Information in Large-Scale Neural Recordings Thaddeus R. Cybulski, Joshua I. Glaser, Adam H. Marblestone, Bradley M. Zamft, Edward S. Boyden, George M. Church, and Konrad P. Kording ; arXiv 2014 (link)

Have a great weekend!