Table of contentsA1 Functional advantages of cell-type heterogeneity in neural circuitsTatyana O. SharpeeA2 Mesoscopic modeling of propagating waves in visual cortexAlain DestexheA3 Dynamics and biomarkers of mental disordersMitsuo KawatoF1 Precise recruitment of spiking output at theta frequencies requires dendritic h-channels in multi-compartment models of oriens-lacunosum/moleculare hippocampal interneuronsVladislav Sekulić, Frances K. SkinnerF2 Kernel methods in reconstruction of current sources from extracellular potentials for single cells and the whole brainsDaniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán SomogyváriF3 The synchronized periods depend on intracellular transcriptional repression mechanisms in circadian clocks.Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Kresimir JosićO1 Assessing irregularity and coordination of spiking-bursting rhythms in central pattern generatorsIrene Elices, David Arroyo, Rafael Levi, Francisco B. Rodriguez, Pablo VaronaO2 Regulation of top-down processing by cortically-projecting parvalbumin positive neurons in basal forebrainEunjin Hwang, Bowon Kim, Hio-Been Han, Tae Kim, James T. McKenna, Ritchie E. Brown, Robert W. McCarley, Jee Hyun ChoiO3 Modeling auditory stream segregation, build-up and bistabilityJames Rankin, Pamela Osborn Popp, John RinzelO4 Strong competition between tonotopic neural ensembles explains pitch-related dynamics of auditory cortex evoked fieldsAlejandro Tabas, André Rupp, Emili Balaguer-BallesterO5 A simple model of retinal response to multi-electrode stimulationMatias I. Maturana, David B. Grayden, Shaun L. Cloherty, Tatiana Kameneva, Michael R. Ibbotson, Hamish MeffinO6 Noise correlations in V4 area correlate with behavioral performance in visual discrimination taskVeronika Koren, Timm Lochmann, Valentin Dragoi, Klaus ObermayerO7 Input-location dependent gain modulation in cerebellar nucleus neuronsMaria Psarrou, Maria Schilstra, Neil Davey, Benjamin Torben-Nielsen, Volker SteuberO8 Analytic solution of cable energy function for cortical axons and dendritesHuiwen Ju, Jiao Yu, Michael L. Hines, Liang Chen, Yuguo YuO9 C. elegans interactome: interactive visualization of Caenorhabditis elegans worm neuronal networkJimin Kim, Will Leahy, Eli ShlizermanO10 Is the model any good? Objective criteria for computational neuroscience model selectionJustas Birgiolas, Richard C. Gerkin, Sharon M. CrookO11 Cooperation and competition of gamma oscillation mechanismsAtthaphon Viriyopase, Raoul-Martin Memmesheimer, Stan GielenO12 A discrete structure of the brain wavesYuri Dabaghian, Justin DeVito, Luca PerottiO13 Direction-specific silencing of the Drosophila gaze stabilization systemAnmo J. Kim, Lisa M. Fenk, Cheng Lyu, Gaby MaimonO14 What does the fruit fly think about values? A model of olfactory associative learningChang Zhao, Yves Widmer, Simon Sprecher,Walter SennO15 Effects of ionic diffusion on power spectra of local field potentials (LFP)Geir Halnes, Tuomo Mäki-Marttunen, Daniel Keller, Klas H. Pettersen,Ole A. Andreassen...

No abstract

Low-resolution models are often used to address macroscopic time and size scales in molecular dynamics simulations of biomolecular systems. Coarse graining is often coupled to knowledge-based parametrization to obtain empirical potentials able to reproduce the system thermodynamic behavior. Here, a minimalist coarse grained (GC) model for the helical structures of proteins is reported. A knowledge-based parametrization strategy is coupled to the explicit inclusion of hydrogen-bonding-related terms, resulting in an accurate reproduction of the structure and dynamics of each single helical type, as well as the internal conformational variables correlation. The proposed strategy of basing the force field terms on real physicochemical interactions is transferable to different secondary structures. Thus, this work, though conclusive for helices, is to be considered the first of a series devoted to the application of the knowledge-based, physicochemical model to extended secondary structures and unstructured proteins.

SecStAnT is available free of charge at secstant.sourceforge.net/. Source code is freely available on request, implemented in Java and supported on Linux, MS Windows and OSX.

Direction selective (DS) ganglion cells (GC) in the retina maintain their tuning across a broad range of light levels. Yet very different circuits can shape their responses from bright to dim light, and their respective contributions are difficult to tease apart. In particular, the contribution of the rod bipolar cell (RBC) primary pathway, a key player in dim light, is unclear. To understand its contribution to DSGC response, we designed an all-optical approach allowing precise manipulation of single retinal neurons. Our system activates single cells in the bipolar cell (BC) layer by two-photon (2P) temporally focused holographic illumination, while recording the activity in the ganglion cell layer by 2P Ca 2 imaging. By doing so, we demonstrate that RBCs provide an asymmetric input to DSGCs, suggesting they contribute to their direction selectivity. Our results suggest that every circuit providing an input to direction selective cells can generate direction selectivity by itself. This hints at a general principle to achieve robust selectivity in sensory areas.A major goal in neuroscience is to understand the circuits that embody the computations performed by sensory neurons. In particular, a striking feature of sensory processing is the ability of neurons to perform the same computation in different contexts. For example, neurons in the piriform cortex represent odor identity while remaining invariant to its exact concentration (Bolding and Franks, 2018). Similarly, neurons in the visual cortex can keep the same orientation tuning curve over different contrasts (Sclar and Freeman, 1982).In the retina, direction selective (DS) ganglion cells (GC) respond selectively to a motion direction in different contexts such as different backgrounds (Chen et al., 2016), different natural scenes (Im and Fried, 2016), and over a broad range of luminosities (Pearson and Kerschensteiner, 2015; Vaney et al., 2001;Yao et al., 2018). Switching the average luminance from dim to bright light will change the dominant circuits that convey visual information inside the retina, leading to major changes in the responses of ganglion cells (Pearson and Kerschensteiner, 2015;Wässle, 2004). For example, cells will change their ON-OFF polarity (Tikidji-Hamburyan et al., 2015). It is therefore particularly striking that direction selectivity remains constant across the ten billion fold change of luminance separating day from night (Yao et al., 2018), despite the involvement of distinct circuits. A major challenge is to understand how this feature is achieved.During daylight conditions, where rods are saturated and cones transmit light input, the major component responsible for direction selectivity is a functional asymmetry. This results either from an asymmetric inhibition or an asymmetric morphology. For example, in the ON-OFF

The increasing trend in the recent literature on coarse grained (CG) models testifies their impact in the study of complex systems. However, the CG model landscape is variegated: even considering a given resolution level, the force fields are very heterogeneous and optimized with very different parametrization procedures. Along the road for standardization of CG models for biopolymers, here we describe a strategy to aid building and optimization of statistics based analytical force fields and its implementation in the software package AsParaGS (Assisted Parameterization platform for coarse Grained modelS). Our method is based on the use and optimization of analytical potentials, optimized by targeting internal variables statistical distributions by means of the combination of different algorithms (i.e., relative entropy driven stochastic exploration of the parameter space and iterative Boltzmann inversion). This allows designing a custom model that endows the force field terms with a physically sound meaning. Furthermore, the level of transferability and accuracy can be tuned through the choice of statistical data set composition. The method-illustrated by means of applications to helical polypeptides-also involves the analysis of two and three variable distributions, and allows handling issues related to the FF term correlations. AsParaGS is interfaced with general-purpose molecular dynamics codes and currently implements the "minimalist" subclass of CG models (i.e., one bead per amino acid, Cα based). Extensions to nucleic acids and different levels of coarse graining are in the course.

Classifying neurons in different types is still an open challenge. In the retina, recent works have taken advantage of the ability to record a large number of cells to classify ganglion cells into different types based on functional information. While the first attempts in this direction used the receptive field properties of each cell to classify them, more recent approaches have proposed to cluster ganglion cells directly based on their response to standard stimuli. These two approaches have not been compared directly. Here we recorded the responses of a large number of ganglion cells and compared two methods for classifying them into types, one based on the receptive field properties, and the other one using their responses to standard stimuli. We show that the stimulus-based approach allows separating more types than the receptive field-based method, leading to a better classification. This better granularity is due to the fact that the stimulus-based method takes into account not only the linear part of ganglion cell function, but also non-linearities. A careful characterization of non-linear processing is thus key to allow functional classification of sensory neurons.

Classifying neurons in different types is still an open challenge. In the retina, recent works have taken advantage of the ability to record a large number of cells to classify ganglion cells into different types based on functional information. While the first attempts in this direction used the receptive field properties of each cell to classify them, more recent approaches have proposed to cluster ganglion cells directly based on their response to standard stimuli. These two approaches have not been compared directly. Here we recorded the responses of a large number of ganglion cells and compared two methods for classifying them into types, one based on the receptive field properties, and the other one using their responses to standard stimuli. We show that the stimulus-based approach allows separating more types than the receptive field-based method, leading to a better classification. This better granularity is due to the fact that the stimulus-based method takes into account not only the linear part of ganglion cell function, but also non-linearities. A careful characterization of non-linear processing is thus key to allow functional classification of sensory neurons.