@article{10383, abstract = {We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles.}, author = {Mallory, S. A. and Šarić, Anđela and Valeriani, C. and Cacciuto, A.}, issn = {1550-2376}, journal = {Physical Review E}, number = {5}, publisher = {American Physical Society}, title = {{Anomalous thermomechanical properties of a self-propelled colloidal fluid}}, doi = {10.1103/physreve.89.052303}, volume = {89}, year = {2014}, } @inproceedings{10793, abstract = {The Hanani–Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this classical result to clustered graphs with two disjoint clusters, and show that a straightforward extension of our result to flat clustered graphs with three or more disjoint clusters is not possible. We also give a new and short proof for a related result by Di Battista and Frati based on the matroid intersection algorithm.}, author = {Fulek, Radoslav and Kynčl, Jan and Malinović, Igor and Pálvölgyi, Dömötör}, booktitle = {International Symposium on Graph Drawing}, issn = {0302-9743}, pages = {428--436}, publisher = {Springer Nature}, title = {{Clustered planarity testing revisited}}, doi = {10.1007/978-3-662-45803-7_36}, volume = {8871}, year = {2014}, } @book{10811, abstract = {Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research.}, editor = {Zažímalová, Eva and Petrášek, Jan and Benková, Eva}, isbn = {9783709115251}, pages = {444}, publisher = {Springer Nature}, title = {{Auxin and Its Role in Plant Development}}, doi = {10.1007/978-3-7091-1526-8}, year = {2014}, } @article{10814, abstract = {We review recent progress towards a rigorous understanding of the excitation spectrum of bosonic quantum many-body systems. In particular, we explain how one can rigorously establish the predictions resulting from the Bogoliubov approximation in the mean field limit. The latter predicts that the spectrum is made up of elementary excitations, whose energy behaves linearly in the momentum for small momentum. This property is crucial for the superfluid behavior of the system. We also discuss a list of open problems in this field.}, author = {Seiringer, Robert}, issn = {1869-7135}, journal = {Jahresbericht der Deutschen Mathematiker-Vereinigung}, keywords = {General Medicine}, pages = {21--41}, publisher = {Springer Nature}, title = {{The excitation spectrum for Bose fluids with weak interactions}}, doi = {10.1365/s13291-014-0083-9}, volume = {116}, year = {2014}, } @article{10815, abstract = {In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest.}, author = {Hashimoto, Masakazu and Morita, Hitoshi and Ueno, Naoto}, issn = {0914-3505}, journal = {Congenital Anomalies}, keywords = {Developmental Biology, Embryology, General Medicine, Pediatrics, Perinatology, and Child Health}, number = {1}, pages = {1--7}, publisher = {Wiley}, title = {{Molecular and cellular mechanisms of development underlying congenital diseases}}, doi = {10.1111/cga.12039}, volume = {54}, year = {2014}, } @article{7598, author = {Tan, Shutang and Xue, Hong-Wei}, issn = {2211-1247}, journal = {Cell Reports}, number = {5}, pages = {1692--1702}, publisher = {Elsevier}, title = {{Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5}}, doi = {10.1016/j.celrep.2014.10.047}, volume = {9}, year = {2014}, } @article{7699, author = {Sweeney, Lora Beatrice Jaeger and Kelley, Darcy B}, issn = {0959-4388}, journal = {Current Opinion in Neurobiology}, number = {10}, pages = {34--41}, publisher = {Elsevier}, title = {{Harnessing vocal patterns for social communication}}, doi = {10.1016/j.conb.2014.06.006}, volume = {28}, year = {2014}, } @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{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{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{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{8022, abstract = {Populations of neurons in motor cortex engage in complex transient dynamics of large amplitude during the execution of limb movements. Traditional network models with stochastically assigned synapses cannot reproduce this behavior. Here we introduce a class of cortical architectures with strong and random excitatory recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from a control theory perspective. Such networks transiently amplify specific activity states and can be used to reliably execute multidimensional movement patterns. Similar to the experimental observations, these transients must be preceded by a steady-state initialization phase from which the network relaxes back into the background state by way of complex internal dynamics. In our networks, excitation and inhibition are as tightly balanced as recently reported in experiments across several brain areas, suggesting inhibitory control of complex excitatory recurrence as a generic organizational principle in cortex.}, author = {Hennequin, Guillaume and Vogels, Tim P and Gerstner, Wulfram}, issn = {0896-6273}, journal = {Neuron}, number = {6}, pages = {1394--1406}, publisher = {Elsevier}, title = {{Optimal control of transient dynamics in balanced networks supports generation of complex movements}}, doi = {10.1016/j.neuron.2014.04.045}, volume = {82}, 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}, } @inproceedings{8044, abstract = {Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system.}, author = {Seiringer, Robert}, booktitle = {Proceeding of the International Congress of Mathematicans}, isbn = {9788961058063}, location = {Seoul, South Korea}, pages = {1175--1194}, publisher = {International Congress of Mathematicians}, title = {{Structure of the excitation spectrum for many-body quantum systems}}, volume = {3}, year = {2014}, } @article{8244, abstract = {Passive immunotherapy with monoclonal antibodies represents a cornerstone of human anticancer therapies, but has not been established in veterinary medicine yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab in human clinical oncology, we present here a “caninized” version of this antibody, can225IgG, for comparative oncology studies. Variable region genes of 225, the murine precursor of cetuximab, were fused with canine constant heavy gamma and kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO) DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected according to productivity and highest specificity in EGFR-coated ELISA. Upon purification with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity, correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing cells was assessed by flow cytometry and immunofluorescence; moreover, binding to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability and proliferation assays, incubation with can225IgG led to significant tumor cell growth inhibition. Moreover, this antibody mediated significant tumor cell killing via phagocytosis in vitro. We thus present here, for the first time, the generation of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like binding site, on the one hand, and the expression of a 91% homologous EGFR molecule in canine cancer, on the other hand, this antibody may be a promising research compound to establish passive immunotherapy in dog patients with cancer.}, author = {Singer, J. and Fazekas, Judit and Wang, W. and Weichselbaumer, M. and Matz, M. and Mader, A. and Steinfellner, W. and Meitz, S. and Mechtcheriakova, D. and Sobanov, Y. and Willmann, M. and Stockner, T. and Spillner, E. and Kunert, R. and Jensen-Jarolim, E.}, issn = {1535-7163}, journal = {Molecular Cancer Therapeutics}, number = {7}, pages = {1777--1790}, publisher = {American Association for Cancer Research}, title = {{Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients}}, doi = {10.1158/1535-7163.mct-13-0288}, volume = {13}, year = {2014}, }