@article{9655,
  abstract     = {Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.},
  author       = {Perkovic, Mario and Kunz, Michael and Endesfelder, Ulrike and Bunse, Stefanie and Wigge, Christoph and Yu, Zhou and Hodirnau, Victor-Valentin and Scheffer, Margot P. and Seybert, Anja and Malkusch, Sebastian and Schuman, Erin M. and Heilemann, Mike and Frangakis, Achilleas S.},
  issn         = {1047-8477},
  journal      = {Journal of Structural Biology},
  number       = {2},
  pages        = {205--213},
  publisher    = {Elsevier},
  title        = {{Correlative light- and electron microscopy with chemical tags}},
  doi          = {10.1016/j.jsb.2014.03.018},
  volume       = {186},
  year         = {2014},
}

@article{9662,
  abstract     = {Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons.},
  author       = {Cheng, Bingqing and Ceriotti, Michele},
  issn         = {1089-7690},
  journal      = {The Journal of Chemical Physics},
  number       = {24},
  publisher    = {AIP Publishing},
  title        = {{Direct path integral estimators for isotope fractionation ratios}},
  doi          = {10.1063/1.4904293},
  volume       = {141},
  year         = {2014},
}

@article{9686,
  abstract     = {It is well known that ultrasonic vibration can soften metals, and this phenomenon has been widely exploited in industrial applications concerning metal forming and bonding. Recent experiments show that the simultaneous application of oscillatory stresses from audible to ultrasonic frequency ranges can lead to not only softening but also significant dislocation annihilation and subgrain formation in metal samples from the nano- to macro-size range. These findings indicate that the existing understanding of ultrasound softening – that the vibrations either impose additional stress waves to augment the quasi-static applied load, or cause heating of the metal, whereas the metal’s intrinsic deformation resistance or mechanism remains unaltered – is far from complete. To understand the softening and the associated enhanced subgrain formation and dislocation annihilation, a new simulator based on the dynamics of dislocation-density functions is employed. This new simulator considers the flux, production and annihilation, as well as the Taylor and elastic interactions between dislocation densities. Softening during vibrations as well as enhanced cell formation is predicted. The simulations reveal the main mechanism for subcell formation under oscillatory loadings to be the enhanced elimination of statistically stored dislocations (SSDs) by the oscillatory stress, leaving behind geometrically necessary dislocations with low Schmid factors which then form the subgrain walls. The oscillatory stress helps the depletion of the SSDs, because the chance for them to meet up and annihilate is increased with reversals of dislocation motions. This is the first simulation effort to successfully predict the cell formation phenomenon under vibratory loadings.},
  author       = {Cheng, Bingqing and Leung, H.S. and Ngan, A.H.W.},
  issn         = {1478-6443},
  journal      = {Philosophical Magazine},
  number       = {16-18},
  pages        = {1845--1865},
  publisher    = {Taylor & Francis},
  title        = {{Strength of metals under vibrations – dislocation-density-function dynamics simulations}},
  doi          = {10.1080/14786435.2014.897008},
  volume       = {95},
  year         = {2014},
}

@article{97,
  abstract     = {The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm).},
  author       = {Higginbotham, Andrew P and Kuemmeth, Ferdinand and Larsen, Thorvald and Fitzpatrick, Mattias and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles},
  journal      = {APS Physics, Physical Review Letters},
  number       = {21},
  publisher    = {American Physical Society},
  title        = {{Antilocalization of coulomb blockade in a Ge/Si nanowire}},
  doi          = {10.1103/PhysRevLett.112.216806},
  volume       = {112},
  year         = {2014},
}

@misc{9722,
  author       = {Lovrics, Anna and Gao, Yu and Juhász, Bianka and Bock, István and Byrne, Helen M. and Dinnyés, András and Kovács, Krisztián},
  publisher    = {Public Library of Science},
  title        = {{Transition probability between TF expression states when Dbx2 inhibits Nkx2.2}},
  doi          = {10.1371/journal.pone.0111430.s006},
  year         = {2014},
}

@misc{9739,
  author       = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Adlam, Ben and Novak, Martin},
  publisher    = {Public Library of Science},
  title        = {{Detailed proofs for “The time scale of evolutionary innovation”}},
  doi          = {10.1371/journal.pcbi.1003818.s001},
  year         = {2014},
}

@misc{9740,
  abstract     = {The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.},
  author       = {Konrad, Matthias and Grasse, Anna V and Tragust, Simon and Cremer, Sylvia},
  publisher    = {Dryad},
  title        = {{Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host}},
  doi          = {10.5061/dryad.vm0vc},
  year         = {2014},
}

@misc{9747,
  abstract     = {Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.},
  author       = {Lagator, Mato and Morgan, Andrew and Neve, Paul and Colegrave, Nick},
  publisher    = {Dryad},
  title        = {{Data from: Role of sex and migration in adaptation to sink environments}},
  doi          = {10.5061/dryad.s42n1},
  year         = {2014},
}

@misc{9752,
  abstract     = {Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.},
  author       = {Simmons, Kristina and Prentice, Jason and Tkačik, Gašper and Homann, Jan and Yee, Heather and Palmer, Stephanie and Nelson, Philip and Balasubramanian, Vijay},
  publisher    = {Dryad},
  title        = {{Data from: Transformation of stimulus correlations by the retina}},
  doi          = {10.5061/dryad.246qg},
  year         = {2014},
}

@article{98,
  abstract     = {Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing.},
  author       = {Higginbotham, Andrew P and Larsen, Thorvald and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles and Kuemmeth, Ferdinand},
  journal      = {Nano Letters},
  number       = {6},
  pages        = {3582 -- 3586},
  publisher    = {American Chemical Society},
  title        = {{Hole spin coherence in a Ge/Si heterostructure nanowire}},
  doi          = {10.1021/nl501242b},
  volume       = {14},
  year         = {2014},
}

@article{6739,
  abstract     = {We explore the relationship between polar and RM codes and we describe a coding scheme which improves upon the performance of the standard polar code at practical block lengths. Our starting point is the experimental observation that RM codes have a smaller error probability than polar codes under MAP decoding. This motivates us to introduce a family of codes that “interpolates” between RM and polar codes, call this family C inter = {C α : α ∈ [0, 1j}, where C α|α=1 is the original polar code, and C α|α=0 is an RM code. Based on numerical observations, we remark that the error probability under MAP decoding is an increasing function of α. MAP decoding has in general exponential complexity, but empirically the performance of polar codes at finite block lengths is boosted by moving along the family Cinter even under low-complexity decoding schemes such as, for instance, belief propagation or successive cancellation list decoder. We demonstrate the performance gain via numerical simulations for transmission over the erasure channel as well as the Gaussian channel.},
  author       = {Mondelli, Marco and Hassani, Hamed and Urbanke, Rudiger},
  issn         = {0090-6778},
  journal      = {IEEE Transactions on Communications},
  number       = {9},
  pages        = {3084--3091},
  publisher    = {IEEE},
  title        = {{From polar to Reed-Muller codes: A technique to improve the finite-length performance}},
  doi          = {10.1109/tcomm.2014.2345069},
  volume       = {62},
  year         = {2014},
}

@inproceedings{6740,
  abstract     = {We describe coding techniques that achieve the capacity of a discrete memoryless asymmetric channel. To do so, we discuss how recent advances in coding for symmetric channels yield more efficient solutions also for the asymmetric case. In more detail, we consider three basic approaches. The first one is Gallager's scheme that concatenates a linear code with a non-linear mapper, in order to bias the input distribution. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Further, we derive a scaling law between the gap to capacity, the cardinality of channel input and output alphabets, and the required size of the mapper. The second one is an integrated approach in which the coding scheme is used both for source coding, in order to create codewords with the capacity-achieving distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third approach is based on an idea due to Böcherer and Mathar and separates completely the two tasks of source coding and channel coding by “chaining” together several codewords. We prove that we can combine any suitable source code with any suitable channel code in order to provide optimal schemes for asymmetric channels. In particular, polar codes and spatially coupled codes fulfill the required conditions.},
  author       = {Mondelli, Marco and Urbanke, Rudiger and Hassani, Hamed},
  booktitle    = {52nd Annual Allerton Conference on Communication, Control, and Computing},
  location     = {Monticello, IL, United States},
  pages        = {789--796},
  publisher    = {IEEE},
  title        = {{How to achieve the capacity of asymmetric channels}},
  doi          = {10.1109/allerton.2014.7028535},
  year         = {2014},
}

@article{6744,
  abstract     = {With the aim of extending the coverage and improving the performance of impulse radio ultra-wideband (UWB) systems, this paper focuses on developing a novel single differential encoded decode and forward (DF) non-cooperative relaying scheme (NCR). To favor simple receiver structures, differential noncoherent detection is employed which enables effective energy capture without any channel estimation. Putting emphasis on the general case of multi-hop relaying, we illustrate an original algorithm for the joint power allocation and path selection (JPAPS), minimizing an approximate expression of the overall bit error rate (BER). In particular, after deriving a closed-form power allocation strategy, the optimal path selection is reduced to a shortest path problem on a connected graph, which can be solved without any topology information with complexity O(N 3 ), N being the number of available relays of the network. An approximate scheme is also presented, which reduces the complexity to O(N 2 ) while showing a negligible performance loss, and for benchmarking purposes, an exhaustive-search based multi-hop DF cooperative strategy is derived. Simulation results for various network setups corroborate the effectiveness of the proposed low-complexity JPAPS algorithm, which favorably compares to existing AF and DF relaying methods.},
  author       = {Mondelli, Marco and Zhou, Qi and Lottici, Vincenzo and Ma, Xiaoli},
  journal      = {IEEE Transactions on Wireless Communications},
  number       = {3},
  pages        = {1397--1409},
  publisher    = {IEEE},
  title        = {{Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications}},
  doi          = {10.1109/twc.2014.020914.130669},
  volume       = {13},
  year         = {2014},
}

@book{6853,
  abstract     = {This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields.},
  author       = {Edelsbrunner, Herbert},
  isbn         = {9-783-3190-5956-3},
  issn         = {2191-5318},
  pages        = {IX, 110},
  publisher    = {Springer Nature},
  title        = {{A Short Course in Computational Geometry and Topology}},
  doi          = {10.1007/978-3-319-05957-0},
  year         = {2014},
}

@techreport{7038,
  author       = {Huszár, Kristóf and Rolinek, Michal},
  pages        = {5},
  publisher    = {IST Austria},
  title        = {{Playful Math - An introduction to mathematical games}},
  year         = {2014},
}

@article{7071,
  abstract     = {Spin and orbital quantum numbers play a key role in the physics of Mott insulators, but in most systems they are connected only indirectly—via the Pauli exclusion principle and the Coulomb interaction. Iridium-based oxides (iridates) introduce strong spin–orbit coupling directly, such that these numbers become entwined together and the Mott physics attains a strong orbital character. In the layered honeycomb iridates this is thought to generate highly spin–anisotropic magnetic interactions, coupling the spin to a given spatial direction of exchange and leading to strongly frustrated magnetism. Here we report a new iridate structure that has the same local connectivity as the layered honeycomb and exhibits striking evidence for highly spin–anisotropic exchange. The basic structural units of this material suggest that a new family of three-dimensional structures could exist, the ‘harmonic honeycomb’ iridates, of which the present compound is the first example.},
  author       = {Modic, Kimberly A and Smidt, Tess E. and Kimchi, Itamar and Breznay, Nicholas P. and Biffin, Alun and Choi, Sungkyun and Johnson, Roger D. and Coldea, Radu and Watkins-Curry, Pilanda and McCandless, Gregory T. and Chan, Julia Y. and Gandara, Felipe and Islam, Z. and Vishwanath, Ashvin and Shekhter, Arkady and McDonald, Ross D. and Analytis, James G.},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Science and Business Media LLC},
  title        = {{Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate}},
  doi          = {10.1038/ncomms5203},
  volume       = {5},
  year         = {2014},
}

@article{7072,
  abstract     = {We investigate the structural and magnetic properties of two molecule-based magnets synthesized from the same starting components. Their different structural motifs promote contrasting exchange pathways and consequently lead to markedly different magnetic ground states. Through examination of their structural and magnetic properties we show that [Cu(pyz)(H2O)(gly)2](ClO4)2 may be considered a quasi-one-dimensional quantum Heisenberg antiferromagnet whereas the related compound [Cu(pyz)(gly)](ClO4), which is formed from dimers of antiferromagnetically interacting Cu2+ spins, remains disordered down to at least 0.03 K in zero field but shows a field-temperature phase diagram reminiscent of that seen in materials showing a Bose-Einstein condensation of magnons.},
  author       = {Lancaster, T. and Goddard, P. A. and Blundell, S. J. and Foronda, F. R. and Ghannadzadeh, S. and Möller, J. S. and Baker, P. J. and Pratt, F. L. and Baines, C. and Huang, L. and Wosnitza, J. and McDonald, R. D. and Modic, Kimberly A and Singleton, J. and Topping, C. V. and Beale, T. A. W. and Xiao, F. and Schlueter, J. A. and Barton, A. M. and Cabrera, R. D. and Carreiro, K. E. and Tran, H. E. and Manson, J. L.},
  issn         = {1079-7114},
  journal      = {Physical Review Letters},
  number       = {20},
  publisher    = {APS},
  title        = {{Controlling magnetic order and quantum disorder in molecule-based magnets}},
  doi          = {10.1103/physrevlett.112.207201},
  volume       = {112},
  year         = {2014},
}

@article{7300,
  abstract     = {Photoinduced electron transfer (PET), which causes pH-dependent quenching of fluorescent dyes, is more effectively introduced by phenolic groups than by amino groups which have been much more commonly used so far. That is demonstrated by fluorescence measurements involving several classes of fluorophores. Electrochemical measurements show that PET in several amino-modified dyes is thermodynamically favorable, even though it was not experimentally found, underlining the importance of kinetic aspects to the process. Consequently, the attachment of phenolic groups allows for fast and simple preparation of a wide selection of fluorescent pH-probes with tailor-made spectral properties, sensitive ranges, and individual advantages, so that a large number of applications can be realized. Fluorophores carrying phenolic groups may also be used for sensing analytes other than pH or molecular switching and signaling.},
  author       = {Aigner, Daniel and Freunberger, Stefan Alexander and Wilkening, Martin and Saf, Robert and Borisov, Sergey M. and Klimant, Ingo},
  issn         = {0003-2700},
  journal      = {Analytical Chemistry},
  number       = {18},
  pages        = {9293--9300},
  publisher    = {ACS},
  title        = {{Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols}},
  doi          = {10.1021/ac502513g},
  volume       = {86},
  year         = {2014},
}

@article{7301,
  abstract     = {Several problems arise at the O2 (positive) electrode in the Li-air battery, including solvent/electrode decomposition and electrode passivation by insulating Li2O2. Progress partially depends on exploring the basic electrochemistry of O2 reduction. Here we describe the effect of complexing-cations on the electrochemical reduction of O2 in DMSO in the presence and absence of a Li salt. The solubility of alkaline peroxides in DMSO is enhanced by the complexing-cations, consistent with their strong interaction with reduced O2. The complexing-cations also increase the rate of the 1-electron O2 reduction to O2•– by up to six-fold (k° = 2.4 ×10–3 to 1.5 × 10–2 cm s–1) whether or not Li+ ions are present. In the absence of Li+, the complexing-cations also promote the reduction of O2•– to O22–. In the presence of Li+ and complexing-cations, and despite the interaction of the reduced O2 with the latter, SERS confirms that the product is still Li2O2.},
  author       = {Li, Chunmei and Fontaine, Olivier and Freunberger, Stefan Alexander and Johnson, Lee and Grugeon, Sylvie and Laruelle, Stéphane and Bruce, Peter G. and Armand, Michel},
  issn         = {1932-7447},
  journal      = {The Journal of Physical Chemistry C},
  number       = {7},
  pages        = {3393--3401},
  publisher    = {ACS},
  title        = {{Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent}},
  doi          = {10.1021/jp4093805},
  volume       = {118},
  year         = {2014},
}

@article{7302,
  abstract     = {Understanding charge carrier transport in Li2O2, the storage material in the non-aqueous Li-O2 battery, is key to the development of this high-energy battery. Here, we studied ionic transport properties and Li self-diffusion in nanocrystalline Li2O2 by conductivity and temperature variable 7Li NMR spectroscopy. Nanostructured Li2O2, characterized by a mean crystallite size of less than 50 nm as estimated from X-ray diffraction peak broadening, was prepared by high-energy ball milling of microcrystalline lithium peroxide with μm sized crystallites. At room temperature the overall conductivity σ of the microcrystalline reference sample turned out to be very low (3.4 × 10−13 S cm−1) which is in agreement with results from temperature-variable 7Li NMR line shape measurements. Ball-milling, however, leads to an increase of σ by approximately two orders of magnitude (1.1 × 10−10 S cm−1); correspondingly, the activation energy decreases from 0.89 eV to 0.82 eV. The electronic contribution σeon, however, is in the order of 9 × 10−12 S cm−1 which makes less than 10% of the total value. Interestingly, 7Li NMR lines of nano-Li2O2 undergo pronounced heterogeneous motional narrowing which manifests in a two-component line shape emerging with increasing temperatures. Most likely, the enhancement in σ can be traced back to the generation of a spin reservoir with highly mobile Li ions; these are expected to reside in the nearest neighbourhood of defects generated or near the structurally disordered and defect-rich interfacial regions formed during mechanical treatment.},
  author       = {Dunst, A. and Epp, V. and Hanzu, I. and Freunberger, Stefan Alexander and Wilkening, M.},
  issn         = {1754-5692},
  journal      = {Energy & Environmental Science},
  number       = {8},
  pages        = {2739--2752},
  publisher    = {RSC},
  title        = {{Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries}},
  doi          = {10.1039/c4ee00496e},
  volume       = {7},
  year         = {2014},
}