@inbook{7743, abstract = {Experimental studies have demonstrated that environmental variation can create genotype‐environment interactions (GEIs) in the traits involved in sexual selection. Understanding the genetic architecture of phenotype across environments will require statistical tests that can describe both changes in genetic variance and covariance across environments. This chapter outlines the theoretical framework for the processes of sexual selection in the wild, identifying key parameters in wild systems, and highlighting the potential effects of the environment. It describes the proposed approaches for the estimation of these key parameters in a quantitative genetic framework within naturally occurring pedigreed populations. The chapter provides a worked example for a range of analysis methods. It aims to provide an overview of the analytical methods that can be used to model GEIs for traits involved in sexual selection in naturally occurring pedigreed populations.}, author = {Robinson, Matthew Richard and Qvarnström, Anna}, booktitle = {Genotype-by-Environment Interactions and Sexual Selection}, editor = {Hunt, John and Hosken, David}, isbn = {9780470671795}, pages = {137--168}, publisher = {Wiley}, title = {{Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations}}, doi = {10.1002/9781118912591.ch6}, year = {2014}, } @article{7744, author = {Robinson, Matthew Richard and Wray, Naomi R. and Visscher, Peter M.}, issn = {0168-9525}, journal = {Trends in Genetics}, number = {4}, pages = {124--132}, publisher = {Elsevier}, title = {{Explaining additional genetic variation in complex traits}}, doi = {10.1016/j.tig.2014.02.003}, volume = {30}, year = {2014}, } @article{7768, abstract = {We investigate the vibrational modes of quasi-two-dimensional disordered colloidal packings of hard colloidal spheres with short-range attractions as a function of packing fraction. Certain properties of the vibrational density of states (vDOS) are shown to correlate with the density and structure of the samples (i.e., in sparsely versus densely packed samples). Specifically, a crossover from dense glassy to sparse gel-like states is suggested by an excess of phonon modes at low frequency and by a variation in the slope of the vDOS with frequency at low frequency. This change in phonon mode distribution is demonstrated to arise largely from localized vibrations that involve individual and/or small clusters of particles with few local bonds. Conventional order parameters and void statistics did not exhibit obvious gel-glass signatures as a function of volume fraction. These mode behaviors and accompanying structural insights offer a potentially new set of indicators for identification of glass-gel transitions and for assignment of gel-like versus glass-like character to a disordered solid material.}, author = {Lohr, Matthew A. and Still, Tim and Ganti, Raman and Gratale, Matthew D. and Davidson, Zoey S. and Aptowicz, Kevin B. and Goodrich, Carl Peter and Sussman, Daniel M. and Yodh, A. G.}, issn = {1539-3755}, journal = {Physical Review E}, number = {6}, publisher = {American Physical Society}, title = {{Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings}}, doi = {10.1103/physreve.90.062305}, volume = {90}, year = {2014}, } @article{7771, abstract = {In their Letter, Schreck, Bertrand, O'Hern and Shattuck [Phys. Rev. Lett. 107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise when contacts are altered. They conclude that there is "no harmonic regime in the large system limit for all compressions" and "at jamming onset for any system size." Their argument rests on the claim that for finite-range repulsive potentials, of the form used in studies of jamming, the breaking or forming of a single contact is sufficient to destroy the linear regime. We dispute these conclusions and argue that linear response is both justified and essential for understanding the nature of the jammed solid. }, author = {Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.}, issn = {0031-9007}, journal = {Physical Review Letters}, number = {4}, publisher = {American Physical Society}, title = {{Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”}}, doi = {10.1103/physrevlett.112.049801}, volume = {112}, year = {2014}, } @article{7772, abstract = {Particle tracking and displacement covariance matrix techniques are employed to investigate the phonon dispersion relations of two-dimensional colloidal glasses composed of soft, thermoresponsive microgel particles whose temperature-sensitive size permits in situ variation of particle packing fraction. Bulk, B, and shear, G, moduli of the colloidal glasses are extracted from the dispersion relations as a function of packing fraction, and variation of the ratio G/B with packing fraction is found to agree quantitatively with predictions for jammed packings of frictional soft particles. In addition, G and B individually agree with numerical predictions for frictional particles. This remarkable level of agreement enabled us to extract an energy scale for the interparticle interaction from the individual elastic constants and to derive an approximate estimate for the interparticle friction coefficient.}, author = {Still, Tim and Goodrich, Carl Peter and Chen, Ke and Yunker, Peter J. and Schoenholz, Samuel and Liu, Andrea J. and Yodh, A. G.}, issn = {1539-3755}, journal = {Physical Review E}, number = {1}, publisher = {American Physical Society}, title = {{Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions}}, doi = {10.1103/physreve.89.012301}, volume = {89}, year = {2014}, } @article{7773, abstract = {For more than a century, physicists have described real solids in terms of perturbations about perfect crystalline order1. Such an approach takes us only so far: a glass, another ubiquitous form of rigid matter, cannot be described in any meaningful sense as a defected crystal2. Is there an opposite extreme to a crystal—a solid with complete disorder—that forms an alternative starting point for understanding real materials? Here, we argue that the solid comprising particles with finite-ranged interactions at the jamming transition3,4,5 constitutes such a limit. It has been shown that the physics associated with this transition can be extended to interactions that are long ranged6. We demonstrate that jamming physics is not restricted to amorphous systems, but dominates the behaviour of solids with surprisingly high order. Just as the free-electron and tight-binding models represent two idealized cases from which to understand electronic structure1, we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming can be set side by side with the physics of crystals to provide an organizing structure for understanding the mechanical properties of solids over the entire spectrum of disorder.}, author = {Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.}, issn = {1745-2473}, journal = {Nature Physics}, number = {8}, pages = {578--581}, publisher = {Springer Nature}, title = {{Solids between the mechanical extremes of order and disorder}}, doi = {10.1038/nphys3006}, volume = {10}, year = {2014}, } @article{7769, abstract = {Athermal packings of soft repulsive spheres exhibit a sharp jamming transition in the thermodynamic limit. Upon further compression, various structural and mechanical properties display clean power-law behavior over many decades in pressure. As with any phase transition, the rounding of such behavior in finite systems close to the transition plays an important role in understanding the nature of the transition itself. The situation for jamming is surprisingly rich: the assumption that jammed packings are isotropic is only strictly true in the large-size limit, and finite-size has a profound effect on the very meaning of jamming. Here, we provide a comprehensive numerical study of finite-size effects in sphere packings above the jamming transition, focusing on stability as well as the scaling of the contact number and the elastic response.}, author = {Goodrich, Carl Peter and Dagois-Bohy, Simon and Tighe, Brian P. and van Hecke, Martin and Liu, Andrea J. and Nagel, Sidney R.}, issn = {1539-3755}, journal = {Physical Review E}, number = {2}, publisher = {American Physical Society}, title = {{Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling}}, doi = {10.1103/physreve.90.022138}, volume = {90}, year = {2014}, } @article{7770, abstract = {Packings of frictionless athermal particles that interact only when they overlap experience a jamming transition as a function of packing density. Such packings provide the foundation for the theory of jamming. This theory rests on the observation that, despite the multitude of disordered configurations, the mechanical response to linear order depends only on the distance to the transition. We investigate the validity and utility of such measurements that invoke the harmonic approximation and show that, despite particles coming in and out of contact, there is a well-defined linear regime in the thermodynamic limit.}, author = {Goodrich, Carl Peter and Liu, Andrea J. and Nagel, Sidney R.}, issn = {1539-3755}, journal = {Physical Review E}, number = {2}, publisher = {American Physical Society}, title = {{Contact nonlinearities and linear response in jammed particulate packings}}, doi = {10.1103/physreve.90.022201}, volume = {90}, year = {2014}, } @article{8021, abstract = {Most excitatory inputs in the mammalian brain are made on dendritic spines, rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical isolation can underlie input-specific synaptic plasticity, providing a raison d'etre for spines. However, recent results indicate that the spine can experience a membrane potential different from that in the parent dendrite, as though the spine neck electrically isolated the spine. Here we use two-photon calcium imaging of mouse neocortical pyramidal neurons to analyze the correlation between the morphologies of spines activated under minimal synaptic stimulation and the excitatory postsynaptic potentials they generate. We find that excitatory postsynaptic potential amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike timing-dependent plasticity protocol, in which two-photon glutamate uncaging over a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine neck and concomitant increases in the amplitude of the evoked spine potentials. Using numerical simulations, we explore the parameter regimes for the spine neck resistance and synaptic conductance changes necessary to explain our observations. Our data, directly correlating synaptic and morphological plasticity, imply that long-necked spines have small or negligible somatic voltage contributions, but that, upon synaptic stimulation paired with postsynaptic activity, they can shorten their necks and increase synaptic efficacy, thus changing the input/output gain of pyramidal neurons. }, author = {Araya, R. and Vogels, Tim P and Yuste, R.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {28}, pages = {E2895--E2904}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Activity-dependent dendritic spine neck changes are correlated with synaptic strength}}, doi = {10.1073/pnas.1321869111}, volume = {111}, year = {2014}, } @article{8023, abstract = {Uniform random sparse network architectures are ubiquitous in computational neuroscience, but the implicit hypothesis that they are a good representation of real neuronal networks has been met with skepticism. Here we used two experimental data sets, a study of triplet connectivity statistics and a data set measuring neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands of model networks. Network architectures comprised three neuron types (excitatory, fast spiking, and nonfast spiking inhibitory) and were created from a set of rules that govern the statistics of the resulting connection types. In a high-dimensional parameter scan, we varied the degree distributions (i.e., how many cells each neuron connects with) and the synaptic weight correlations of synapses from or onto the same neuron. These variations converted initially uniform random and homogeneously connected networks, in which every neuron sent and received equal numbers of synapses with equal synaptic strength distributions, to highly heterogeneous networks in which the number of synapses per neuron, as well as average synaptic strength of synapses from or to a neuron were variable. By evaluating the impact of each variable on the network structure and dynamics, and their similarity to the experimental data, we could falsify the uniform random sparse connectivity hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis in 8 cases. Twenty-one parameters had no substantial impact on the results of the test protocols we used.}, author = {Tomm, Christian and Avermann, Michael and Petersen, Carl and Gerstner, Wulfram and Vogels, Tim P}, issn = {1522-1598}, journal = {Journal of Neurophysiology}, number = {8}, pages = {1801--1814}, publisher = {American Physiological Society}, title = {{Connection-type-specific biases make uniform random network models consistent with cortical recordings}}, doi = {10.1152/jn.00629.2013}, volume = {112}, year = {2014}, }