TY - JOUR AB - We show that bimolecular reactions between species confined to the surfaces of nanoparticles can be manipulated by the nature of the linker, as well as by the curvature of the underlying particles. AU - Zdobinsky, Tino AU - Sankar Maiti, Pradipta AU - Klajn, Rafal ID - 13403 IS - 7 JF - Journal of the American Chemical Society KW - Colloid and Surface Chemistry KW - Biochemistry KW - General Chemistry KW - Catalysis SN - 0002-7863 TI - Support curvature and conformational freedom control chemical reactivity of immobilized species VL - 136 ER - TY - JOUR AB - The sensitivities of high-harmonic generation (HHG) and strong-field ionization (SFI) to coupled electronic and nuclear dynamics are studied, using the nitric oxide (NO) molecule as an example. A coherent superposition of electronic and rotational states of NO is prepared by impulsive stimulated Raman scattering and probed by simultaneous detection of HHG and SFI yields. We observe a fourfold higher sensitivity of high-harmonic generation to electronic dynamics and attribute it to the presence of inelastic quantum paths connecting coherently related electronic states [Kraus et al., Phys. Rev. Lett.111, 243005 (2013)]. Whereas different harmonic orders display very different sensitivities to rotational or electronic dynamics, strong-field ionization is found to be most sensitive to electronic motion. We introduce a general theoretical formalism for high-harmonic generation from coupled nuclear-electronic wave packets. We show that the unequal sensitivities of different harmonic orders to electronic or rotational dynamics result from the angle dependence of the photorecombination matrix elements which encode several autoionizing and shape resonances in the photoionization continuum of NO. We further study the dependence of rotational and electronic coherences on the intensity of the excitation pulse and support the observations with calculations. AU - Baykusheva, Denitsa Rangelova AU - Kraus, Peter M. AU - Zhang, Song Bin AU - Rohringer, Nina AU - Wörner, Hans Jakob ID - 14018 JF - Faraday Discussions KW - Physical and Theoretical Chemistry SN - 1359-6640 TI - The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics VL - 171 ER - TY - JOUR AB - The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra of deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺) to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2 rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity. AU - Vasilatou, K. AU - Michaud, J. M. AU - Baykusheva, Denitsa Rangelova AU - Grassi, G. AU - Merkt, F. ID - 14019 IS - 6 JF - The Journal of Chemical Physics KW - Physical and Theoretical Chemistry KW - General Physics and Astronomy SN - 0021-9606 TI - The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra VL - 141 ER - TY - JOUR AB - We present the detailed analysis of a new two-pulse orientation scheme that achieves macroscopic field-free orientation at the high particle densities required for attosecond and high-harmonic spectroscopies (Kraus et al 2013 arXiv:1311.3923). Carbon monoxide molecules are oriented by combining one-colour and delayed two-colour non-resonant femtosecond laser pulses. High-harmonic generation is used to probe the oriented wave-packet dynamics and reveals that a very high degree of orientation (Nup/Ntotal = 0.73–0.82) is achieved. We further extend this approach to orienting carbonyl sulphide molecules. We show that the present two-pulse scheme selectively enhances orientation created by the hyperpolarizability interaction whereas the ionization-depletion mechanism plays no role. We further control and optimize orientation through the delay between the one- and two-colour pump pulses. Finally, we demonstrate a complementary encoding of electronic-structure features, such as shape resonances, in the even- and odd-harmonic spectrum. The achieved progress makes two-pulse field-free orientation an attractive tool for a broad class of time-resolved measurements. AU - Kraus, P M AU - Baykusheva, Denitsa Rangelova AU - Wörner, H J ID - 14021 IS - 12 JF - Journal of Physics B: Atomic, Molecular and Optical Physics KW - Condensed Matter Physics KW - Atomic and Molecular Physics KW - and Optics SN - 0953-4075 TI - Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules VL - 47 ER - TY - JOUR AB - We report the observation of macroscopic field-free orientation, i.e., more than 73% of CO molecules pointing in the same direction. This is achieved through an all-optical scheme operating at high particle densities (>10(17)  cm(-3)) that combines one-color (ω) and two-color (ω+2ω) nonresonant femtosecond laser pulses. We show that the achieved orientation solely relies on the hyperpolarizability interaction as opposed to an ionization-depletion mechanism, thus, opening a wide range of applications. The achieved strong orientation enables us to reveal the molecular-frame anisotropies of the photorecombination amplitudes and phases caused by a shape resonance. The resonance appears as a local maximum in the even-harmonic emission around 28 eV. In contrast, the odd-harmonic emission is suppressed in this spectral region through the combined effects of an asymmetric photorecombination phase and a subcycle Stark effect, generic for polar molecules, that we experimentally identify. AU - Kraus, P. M. AU - Baykusheva, Denitsa Rangelova AU - Wörner, H. J. ID - 14020 IS - 2 JF - Physical Review Letters KW - General Physics and Astronomy SN - 0031-9007 TI - Two-pulse field-free orientation reveals anisotropy of molecular shape resonance VL - 113 ER - TY - JOUR AB - Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help. AU - Chatterjee, Krishnendu AU - Henzinger, Monika H AU - Krinninger, Sebastian AU - Nanongkai, Danupon ID - 535 IS - 3 JF - Algorithmica TI - Polynomial-time algorithms for energy games with special weight structures VL - 70 ER - TY - CONF AB - We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set. AU - Zobel, Valentin AU - Reininghaus, Jan AU - Hotz, Ingrid ID - 10886 SN - 1612-3786 T2 - Topological Methods in Data Analysis and Visualization III TI - Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature ER - TY - CHAP AB - Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo. AU - Smutny, Michael AU - Behrndt, Martin AU - Campinho, Pedro AU - Ruprecht, Verena AU - Heisenberg, Carl-Philipp J ED - Nelson, Celeste ID - 6178 SN - 1064-3745 T2 - Tissue Morphogenesis TI - UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo VL - 1189 ER - TY - JOUR AB - 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. AU - Seiringer, Robert ID - 10814 JF - Jahresbericht der Deutschen Mathematiker-Vereinigung KW - General Medicine SN - 0012-0456 TI - The excitation spectrum for Bose fluids with weak interactions VL - 116 ER - TY - CHAP AB - The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption. AU - Günther, David AU - Reininghaus, Jan AU - Seidel, Hans-Peter AU - Weinkauf, Tino ED - Bremer, Peer-Timo ED - Hotz, Ingrid ED - Pascucci, Valerio ED - Peikert, Ronald ID - 10817 SN - 1612-3786 T2 - Topological Methods in Data Analysis and Visualization III. TI - Notes on the simplification of the Morse-Smale complex ER - TY - THES AB - In this thesis I studied various individual and social immune defences employed by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi. The first two chapters of this thesis address the phenomenon of 'social immunisation'. Social immunisation, that is the immunological protection of group members due to social contact to a pathogen-exposed nestmate, has been described in various social insect species against different types of pathogens. However, in the case of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation exists at all. Its underlying mechanisms r any other properties were, however, unknown. In the first chapter of this thesis I identified the mechanistic basis of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium. I could show that nestmates of a pathogen-exposed individual contract low-level infections due to social interactions. These low-level infections are, however, non-lethal and cause an active stimulation of the immune system, which protects the nestmates upon subsequent pathogen encounters. In the second chapter of this thesis I investigated the specificity and colony level effects of social immunisation. I demonstrated that the protection conferred by social immunisation is highly specific, protecting ants only against the same pathogen strain. In addition, depending on the respective context, social immunisation may even cause fitness costs. I further showed that social immunisation crucially affects sanitary behaviour and disease dynamics within ant groups. In the third chapter of this thesis I studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic fungi, research concerning host fitness consequence is sparse. I showed that highly Laboulbenia-infected ants sustain fitness costs under resource limitation, however, gain fitness benefits when exposed to an entomopathogenus fungus. These effects are probably cause by a prophylactic upregulation of behavioural as well as physiological immune defences in highly infected ants. AU - Konrad, Matthias ID - 1395 SN - 2663-337X TI - Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus ER - TY - THES AB - Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants. AU - Marhavá, Petra ID - 1402 SN - 2663-337X TI - Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana ER - TY - JOUR AB - Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm. AU - Edelsbrunner, Herbert AU - Pausinger, Florian ID - 2255 IS - 1 JF - Journal of Mathematical Imaging and Vision SN - 09249907 TI - Stable length estimates of tube-like shapes VL - 50 ER - TY - CONF AB - Motivated by topological Tverberg-type problems, we consider multiple (double, triple, and higher multiplicity) selfintersection points of maps from finite simplicial complexes (compact polyhedra) into ℝd and study conditions under which such multiple points can be eliminated. The most classical case is that of embeddings (i.e., maps without double points) of a κ-dimensional complex K into ℝ2κ. For this problem, the work of van Kampen, Shapiro, and Wu provides an efficiently testable necessary condition for embeddability (namely, vanishing of the van Kampen ob-struction). For κ ≥ 3, the condition is also sufficient, and yields a polynomial-time algorithm for deciding embeddability: One starts with an arbitrary map f : K→ℝ2κ, which generically has finitely many double points; if k ≥ 3 and if the obstruction vanishes then one can successively remove these double points by local modifications of the map f. One of the main tools is the famous Whitney trick that permits eliminating pairs of double points of opposite intersection sign. We are interested in generalizing this approach to intersection points of higher multiplicity. We call a point y 2 ℝd an r-fold Tverberg point of a map f : Kκ →ℝd if y lies in the intersection f(σ1)∩. ∩f(σr) of the images of r pairwise disjoint simplices of K. The analogue of (non-)embeddability that we study is the problem Tverbergκ r→d: Given a κ-dimensional complex K, does it satisfy a Tverberg-type theorem with parameters r and d, i.e., does every map f : K κ → ℝd have an r-fold Tverberg point? Here, we show that for fixed r, κ and d of the form d = rm and k = (r-1)m, m ≥ 3, there is a polynomial-time algorithm for deciding this (based on the vanishing of a cohomological obstruction, as in the case of embeddings). Our main tool is an r-fold analogue of the Whitney trick: Given r pairwise disjoint simplices of K such that the intersection of their images contains two r-fold Tverberg points y+ and y- of opposite intersection sign, we can eliminate y+ and y- by a local isotopy of f. In a subsequent paper, we plan to develop this further and present a generalization of the classical Haeiger-Weber Theorem (which yields a necessary and sufficient condition for embeddability of κ-complexes into ℝd for a wider range of dimensions) to intersection points of higher multiplicity. AU - Mabillard, Isaac AU - Wagner, Uli ID - 2159 T2 - Proceedings of the Annual Symposium on Computational Geometry TI - Eliminating Tverberg points, I. An analogue of the Whitney trick ER - TY - JOUR AB - Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution. AU - Novak, Sebastian ID - 2023 IS - 24 JF - Ecology and Evolution TI - Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution VL - 4 ER - TY - CONF AB - While fixing concurrency bugs, program repair algorithms may introduce new concurrency bugs. We present an algorithm that avoids such regressions. The solution space is given by a set of program transformations we consider in the repair process. These include reordering of instructions within a thread and inserting atomic sections. The new algorithm learns a constraint on the space of candidate solutions, from both positive examples (error-free traces) and counterexamples (error traces). From each counterexample, the algorithm learns a constraint necessary to remove the errors. From each positive examples, it learns a constraint that is necessary in order to prevent the repair from turning the trace into an error trace. We implemented the algorithm and evaluated it on simplified Linux device drivers with known bugs. AU - Cerny, Pavol AU - Henzinger, Thomas A AU - Radhakrishna, Arjun AU - Ryzhyk, Leonid AU - Tarrach, Thorsten ID - 2218 SN - 978-331908866-2 TI - Regression-free synthesis for concurrency VL - 8559 ER - TY - CONF AB - Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing. In this paper, we study compositional properties of the ioco-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the ioco conformance relation, the resulting methodology can be applied to a broader class of systems. AU - Daca, Przemyslaw AU - Henzinger, Thomas A AU - Krenn, Willibald AU - Nickovic, Dejan ID - 2167 SN - 2159-4848 T2 - IEEE 7th International Conference on Software Testing, Verification and Validation TI - Compositional specifications for IOCO testing ER - TY - CONF AB - We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems.We focus on qualitative properties forMDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation ofMDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.We present an automated technique for assume-guarantee style reasoning for compositional analysis ofMDPs with qualitative properties by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. AU - Chatterjee, Krishnendu AU - Chmelik, Martin AU - Daca, Przemyslaw ID - 2063 TI - CEGAR for qualitative analysis of probabilistic systems VL - 8559 ER - TY - JOUR AB - Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria. AU - Mitosch, Karin AU - Bollenbach, Tobias ID - 2001 IS - 6 JF - Environmental Microbiology Reports TI - Bacterial responses to antibiotics and their combinations VL - 6 ER - TY - CONF AB - NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). Security proofs and attacks for NMAC can typically be lifted to HMAC. NMAC was introduced by Bellare, Canetti and Krawczyk [Crypto'96], who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, assuming that (1) f is a PRF and (2) the function we get when cascading f is weakly collision-resistant. Unfortunately, HMAC is typically instantiated with cryptographic hash functions like MD5 or SHA-1 for which (2) has been found to be wrong. To restore the provable guarantees for NMAC, Bellare [Crypto'06] showed its security based solely on the assumption that f is a PRF, albeit via a non-uniform reduction. - Our first contribution is a simpler and uniform proof for this fact: If f is an ε-secure PRF (against q queries) and a δ-non-adaptively secure PRF (against q queries), then NMAC f is an (ε+ℓqδ)-secure PRF against q queries of length at most ℓ blocks each. - We then show that this ε+ℓqδ bound is basically tight. For the most interesting case where ℓqδ ≥ ε we prove this by constructing an f for which an attack with advantage ℓqδ exists. This also violates the bound O(ℓε) on the PRF-security of NMAC recently claimed by Koblitz and Menezes. - Finally, we analyze the PRF-security of a modification of NMAC called NI [An and Bellare, Crypto'99] that differs mainly by using a compression function with an additional keying input. This avoids the constant rekeying on multi-block messages in NMAC and allows for a security proof starting by the standard switch from a PRF to a random function, followed by an information-theoretic analysis. We carry out such an analysis, obtaining a tight ℓq2/2 c bound for this step, improving over the trivial bound of ℓ2q2/2c. The proof borrows combinatorial techniques originally developed for proving the security of CBC-MAC [Bellare et al., Crypto'05]. AU - Gazi, Peter AU - Pietrzak, Krzysztof Z AU - Rybar, Michal ED - Garay, Juan ED - Gennaro, Rosario ID - 2082 IS - 1 TI - The exact PRF-security of NMAC and HMAC VL - 8616 ER - TY - JOUR AB - Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the embryo along its left-right (LR) axis. Regional differences in cell shape within the lumen-lining KV epithelium are essential for its LR patterning function. However, the processes by which KV cells acquire their characteristic shapes are largely unknown. Here, we show that the notochord induces regional differences in cell shape within KV by triggering extracellular matrix (ECM) accumulation adjacent to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen growth. Our study provides mechanistic insight into the processes by which KV translates global embryonic patterning into regional cell shape differences required for its LR symmetry-breaking function. AU - Compagnon, Julien AU - Barone, Vanessa AU - Rajshekar, Srivarsha AU - Kottmeier, Rita AU - Pranjic-Ferscha, Kornelija AU - Behrndt, Martin AU - Heisenberg, Carl-Philipp J ID - 1912 IS - 6 JF - Developmental Cell TI - The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ VL - 31 ER - TY - JOUR AB - Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors that sense growth factors and hormones and regulate a variety of cell behaviours in health and disease. Contactless activation of RTKs with spatial and temporal precision is currently not feasible. Here, we generated RTKs that are insensitive to endogenous ligands but can be selectively activated by low-intensity blue light. We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome photoreceptors of stramenopiles resulted in robust activation of the fibroblast growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and rearranged during transfection (RET). In human cancer and endothelial cells, light induced cellular signalling with spatial and temporal precision. Furthermore, light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic approach to actuate cellular signals and manipulate cell behaviour. AU - Grusch, Michael AU - Schelch, Karin AU - Riedler, Robert AU - Gschaider-Reichhart, Eva AU - Differ, Christopher AU - Berger, Walter AU - Inglés Prieto, Álvaro AU - Janovjak, Harald L ID - 2084 IS - 15 JF - EMBO Journal TI - Spatio-temporally precise activation of engineered receptor tyrosine kinases by light VL - 33 ER - TY - CONF AB - We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in ℝ3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, i.e., an essential curve in the boundary of X bounding a disk in S3 nX with length bounded by a computable function of the number of tetrahedra of X. AU - Matoušek, Jiří AU - Sedgwick, Eric AU - Tancer, Martin AU - Wagner, Uli ID - 2157 T2 - Proceedings of the Annual Symposium on Computational Geometry TI - Embeddability in the 3 sphere is decidable ER - TY - CONF AB - PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations. AU - Bauer, Ulrich AU - Kerber, Michael AU - Reininghaus, Jan AU - Wagner, Hubert ID - 10894 SN - 0302-9743 T2 - ICMS 2014: International Congress on Mathematical Software TI - PHAT – Persistent Homology Algorithms Toolbox VL - 8592 ER - TY - GEN AB - Simulation is an attractive alternative for language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. For non-deterministic automata, while language inclusion is PSPACE-complete, simulation can be computed in polynomial time. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. Again, while fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable for mean-payoff automata and the decidability is open for discounted-sum automata, whereas the (quantitative) simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial time algorithms. In this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games. For example, whereas for mean-payoff and discounted-sum games, the players do not need memory to play optimally; we show in contrast that for simulation games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal strategies for both players require infinite memory in general, and (ii) for discounted-sum objectives, optimal strategies need not exist for both players. While the simulation games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory requirements for mean-payoff objectives) as compared to their counterpart without Büchi acceptance conditions, we still present pseudo-polynomial time algorithms to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff and weighted discounted-sum automata. AU - Chatterjee, Krishnendu AU - Henzinger, Thomas A AU - Otop, Jan AU - Velner, Yaron ID - 5428 SN - 2664-1690 TI - Quantitative fair simulation games ER - TY - JOUR AU - Cremer, Sylvia ID - 1887 JF - Zoologie TI - Gemeinsame Krankheitsabwehr in Ameisengesellschaften ER - TY - JOUR AB - The cerebral cortex, the seat of our cognitive abilities, is composed of an intricate network of billions of excitatory projection and inhibitory interneurons. Postmitotic cortical neurons are generated by a diverse set of neural stem cell progenitors within dedicated zones and defined periods of neurogenesis during embryonic development. Disruptions in neurogenesis can lead to alterations in the neuronal cytoarchitecture, which is thought to represent a major underlying cause for several neurological disorders, including microcephaly, autism and epilepsy. Although a number of signaling pathways regulating neurogenesis have been described, the precise cellular and molecular mechanisms regulating the functional neural stem cell properties in cortical neurogenesis remain unclear. Here, we discuss the most up-to-date strategies to monitor the fundamental mechanistic parameters of neuronal progenitor proliferation, and recent advances deciphering the logic and dynamics of neurogenesis. AU - Postiglione, Maria P AU - Hippenmeyer, Simon ID - 2175 IS - 3 JF - Future Neurology SN - 1479-6708 TI - Monitoring neurogenesis in the cerebral cortex: an update VL - 9 ER - TY - JOUR AB - Deposits of phosphorylated tau protein and convergence of pathology in the hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed to evaluate whether regional and cellular vulnerability patterns in the hippocampus distinguish tauopathies or are influenced by their concomitant presence. Methods: We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal subregions/layers in individuals with Alzheimer's disease (AD)-related neurofibrillary degeneration (n = 40), Pick's disease (n = 8), progressive supranuclear palsy (n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n = 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly (n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis. Results: Our study reveals disease-specific hot spots and regional selective vulnerability for these disorders. The pattern of hippocampal AD-related tau pathology is strongly influenced by concomitant AGD. Mathematical analysis reveals that hippocampal involvement in primary tauopathies is distinguishable from early-stage AD-related neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies, which primarily do not affect the hippocampus. These hot spots can be shifted to other regions by the co-occurrence of tauopathies like AGD. Our observations support the notion that globular glial tauopathies and tau-astrogliopathy of the elderly are distinct entities. AU - Milenković, Ivan AU - Petrov, Tatjana AU - Kovács, Gábor ID - 1913 IS - 5-6 JF - Dementia and Geriatric Cognitive Disorders SN - 1420-8008 TI - Patterns of hippocampal tau pathology differentiate neurodegenerative dementias VL - 38 ER - TY - CONF AB - The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue statistics of large real and complex Hermitian matrices with independent, identically distributed entries are universal in a sense that they depend only on the symmetry class of the matrix and otherwise are independent of the details of the distribution. We present the recent solution to this half-century old conjecture. We explain how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also show related results for log-gases that represent a universal model for strongly correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss the extensions of these universality results to more realistic physical systems such as random band matrices. AU - Erdös, László ID - 1507 T2 - Proceedings of the International Congress of Mathematicians TI - Random matrices, log-gases and Hölder regularity VL - 3 ER - TY - CONF AB - 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. AU - Seiringer, Robert ID - 8044 SN - 9788961058063 T2 - Proceeding of the International Congress of Mathematicans TI - Structure of the excitation spectrum for many-body quantum systems VL - 3 ER - TY - CONF AB - Transfer learning has received a lot of attention in the machine learning community over the last years, and several effective algorithms have been developed. However, relatively little is known about their theoretical properties, especially in the setting of lifelong learning, where the goal is to transfer information to tasks for which no data have been observed so far. In this work we study lifelong learning from a theoretical perspective. Our main result is a PAC-Bayesian generalization bound that offers a unified view on existing paradigms for transfer learning, such as the transfer of parameters or the transfer of low-dimensional representations. We also use the bound to derive two principled lifelong learning algorithms, and we show that these yield results comparable with existing methods. AU - Pentina, Anastasia AU - Lampert, Christoph ID - 2160 TI - A PAC-Bayesian bound for Lifelong Learning VL - 32 ER - TY - THES AB - A variety of developmental and disease related processes depend on epithelial cell sheet spreading. In order to gain insight into the biophysical mechanism(s) underlying the tissue morphogenesis we studied the spreading of an epithelium during the early development of the zebrafish embryo. In zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk cell to completely engulf it at the end of gastrulation. Previous studies have proposed that an actomyosin ring forming within the yolk syncytial layer (YSL) acts as purse string that through constriction along its circumference pulls on the margin of the EVL. Direct biophysical evidence for this hypothesis has however been missing. The aim of the thesis was to understand how the actomyosin ring may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate the spreading of the epithelium. Using laser ablation to measure cortical tension within the actomyosin ring we found an anisotropic tension distribution, which was highest along the circumference of the ring. However the low degree of anisotropy was incompatible with the actomyosin ring functioning as a purse string only. Additionally, we observed retrograde cortical flow from vegetal parts of the ring into the EVL margin. Interpreting the experimental data using a theoretical distribution that models the tissues as active viscous gels led us to proposen that the actomyosin ring has a twofold contribution to EVL epiboly. It not only acts as a purse string through constriction along its circumference, but in addition constriction along the width of the ring generates pulling forces through friction-resisted cortical flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly proceeded normally indicating that the flow-friction mechanism is sufficient to drive the process. Aiming to understand what cellular mechanism(s) may facilitate the spreading of the epithelium we found that tension-oriented EVL cell divisions limit tissue anisotropy by releasing tension along the division axis and promote epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions in which oriented-cell division is impaired or the epithelium is mechanically challenged. Taken together our study of EVL epiboly suggests a novel mechanism of force generation for actomyosin rings through friction-resisted cortical flow and highlights the importance of tension-oriented cell divisions in epithelial morphogenesis. AU - Behrndt, Martin ID - 1403 TI - Forces driving epithelial spreading in zebrafish epiboly ER - TY - CHAP AB - Im Rahmen meiner Arbeit mit der kollektiven Krankheitsabwehr in Ameisengesellschaften interessiert mich vor allem, wie sich die Kolonien als Ganzes gegen Krankheiten wehren können. Warum ist dieses Thema der Krankheitsdynamik in Gruppen so wichtig? Ein Vergleich von solitär lebenden Individuen mit Individuen, die in sozialen Gruppen zusammenleben, zeigt die Kosten und die Vorteile des Gruppenlebens: Einerseits haben Individuen in sozialen Gruppen aufgrund der hohen Dichte, in der die Tiere zusammenleben, den hohen Interaktionsraten, die sie miteinander haben, und der engen Verwandtschaft, die sie verbindet, ein höheres Ansteckungsrisiko. Andererseits kann die individuelle Krankheitsabwehr durch die kollektive Abwehr in den Gruppen ergänzt werden. AU - Cremer, Sylvia ID - 1888 SN - 2366-2875 T2 - Soziale Insekten in einer sich wandelnden Welt TI - Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie der Wissenschaften VL - 43 ER - TY - GEN AB - The classical sphere packing problem asks for the best (infinite) arrangement of non-overlapping unit balls which cover as much space as possible. We define a generalized version of the problem, where we allow each ball a limited amount of overlap with other balls. We study two natural choices of overlap measures and obtain the optimal lattice packings in a parameterized family of lattices which contains the FCC, BCC, and integer lattice. AU - Iglesias Ham, Mabel AU - Kerber, Michael AU - Uhler, Caroline ID - 2012 T2 - arXiv TI - Sphere packing with limited overlap ER - TY - JOUR AB - DNA has become a prime material for assembling complex three-dimensional objects that promise utility in various areas of application. However, achieving user-defined goals with DNA objects has been hampered by the difficulty to prepare them at arbitrary concentrations and in user-defined solution conditions. Here, we describe a method that solves this problem. The method is based on poly(ethylene glycol)-induced depletion of species with high molecular weight. We demonstrate that our method is applicable to a wide spectrum of DNA shapes and that it achieves excellent recovery yields of target objects up to 97 %, while providing efficient separation from non-integrated DNA strands. DNA objects may be prepared at concentrations up to the limit of solubility, including the possibility for bringing DNA objects into a solid phase. Due to the fidelity and simplicity of our method we anticipate that it will help to catalyze the development of new types of applications that use self-assembled DNA objects. AU - Stahl, Evi AU - Martin, Thomas AU - Praetorius, Florian M AU - Dietz, Hendrik ID - 14301 IS - 47 JF - Angewandte Chemie International Edition SN - 1433-7851 TI - Facile and scalable preparation of pure and dense DNA origami solutions VL - 126 ER - TY - JOUR AU - Sweeney, Lora Beatrice Jaeger AU - Kelley, Darcy B ID - 7699 IS - 10 JF - Current Opinion in Neurobiology SN - 0959-4388 TI - Harnessing vocal patterns for social communication VL - 28 ER - TY - JOUR AB - We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential. AU - Guo, Yujin AU - Seiringer, Robert ID - 2281 IS - 2 JF - Letters in Mathematical Physics TI - On the mass concentration for Bose-Einstein condensates with attractive interactions VL - 104 ER - TY - JOUR AB - Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such “K-pairwise” models—being systematic extensions of the previously used pairwise Ising models—provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population's capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction. AU - Tkacik, Gasper AU - Marre, Olivier AU - Amodei, Dario AU - Schneidman, Elad AU - Bialek, William AU - Berry, Michael ID - 2257 IS - 1 JF - PLoS Computational Biology SN - 1553734X TI - Searching for collective behavior in a large network of sensory neurons VL - 10 ER - TY - JOUR AB - The copper-catalyzed diboration of ketones followed by an acid-catalyzed elimination leads to the formation of 1,1-disubstituted and trisubstituted vinyl boronate esters with moderate to good yields and selectivity. Addition of tosic acid to the crude diboration products provides the corresponding vinyl boronate esters upon elimination. The trisubstituted vinyl boronate esters are formed as the (Z)-olefin isomer, which was established by subjecting the products to a Suzuki–Miyaura coupling reaction to obtain alkenes of known geometry. AU - Guan, Weiye AU - Michael, Alicia Kathleen AU - McIntosh, Melissa L. AU - Koren-Selfridge, Liza AU - Scott, John P. AU - Clark, Timothy B. ID - 15161 IS - 15 JF - The Journal of Organic Chemistry KW - Organic Chemistry SN - 0022-3263 TI - Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters VL - 79 ER - TY - JOUR AB - Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses. AU - Stroeymeyt, Nathalie AU - Casillas Perez, Barbara E AU - Cremer, Sylvia ID - 1999 IS - 1 JF - Current Opinion in Insect Science TI - Organisational immunity in social insects VL - 5 ER - TY - JOUR AB - Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation. AU - Mognetti, B. M. AU - Šarić, Anđela AU - Angioletti-Uberti, S. AU - Cacciuto, A. AU - Valeriani, C. AU - Frenkel, D. ID - 10384 IS - 24 JF - Physical Review Letters KW - general physics and astronomy SN - 0031-9007 TI - Living clusters and crystals from low-density suspensions of active colloids VL - 111 ER - TY - JOUR AB - In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface. AU - Šarić, Anđela AU - Cacciuto, Angelo ID - 10386 IS - 29 JF - Soft Matter KW - condensed matter physics KW - general chemistry SN - 1744-683X TI - Self-assembly of nanoparticles adsorbed on fluid and elastic membranes VL - 9 ER - TY - JOUR AB - We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials. AU - Napoli, Joseph A. AU - Šarić, Anđela AU - Cacciuto, Angelo ID - 10385 IS - 37 JF - Soft Matter KW - condensed matter physics KW - general chemistry SN - 1744-683X TI - Collapsing nanoparticle-laden nanotubes VL - 9 ER - TY - JOUR AB - Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable. AU - Schlögl, Alois AU - Jonas, Peter M AU - Schmidt-Hieber, C. AU - Guzman, S. J. ID - 10396 IS - SI-1-Track-G JF - Biomedical Engineering / Biomedizinische Technik KW - biomedical engineering KW - data analysis KW - free software SN - 0013-5585 TI - Stimfit: A fast visualization and analysis environment for cellular neurophysiology VL - 58 ER - TY - CONF AB - Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures. AU - Polshyn, Hryhoriy AU - Budakian, Raffi AU - Gu, Genda ID - 10749 IS - 1 SN - 0003-0503 T2 - APS March Meeting 2013 TI - Cantilever micro-susceptometry of mesoscopic Bi2212 samples VL - 58 ER - TY - JOUR AB - Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. AU - Vanneste, Steffen AU - Friml, Jiří ID - 10895 IS - 4 JF - Plants KW - Plant Science KW - Ecology KW - Ecology KW - Evolution KW - Behavior and Systematics SN - 2223-7747 TI - Calcium: The missing link in auxin action VL - 2 ER - TY - CONF AB - A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered. AU - Haas, Andreas AU - Lippautz, Michael AU - Henzinger, Thomas A AU - Payer, Hannes AU - Sokolova, Ana AU - Kirsch, Christoph M. AU - Sezgin, Ali ID - 10898 IS - 5 SN - 978-145032053-5 T2 - Proceedings of the ACM International Conference on Computing Frontiers - CF '13 TI - Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation ER - TY - CHAP AU - Barton, Nicholas H ID - 10899 KW - Adaptive landscape KW - Cline KW - Coalescent process KW - Gene flow KW - Hybrid zone KW - Local adaptation KW - Natural selection KW - Neutral theory KW - Population structure KW - Speciation SN - 978-0-12-384720-1 T2 - Encyclopedia of Biodiversity TI - Differentiation ER - TY - JOUR AB - Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs. AU - Liang, Yun AU - Franks, Tobias M. AU - Marchetto, Maria C. AU - Gage, Fred H. AU - HETZER, Martin W ID - 11086 IS - 2 JF - PLoS Genetics KW - Cancer Research KW - Genetics (clinical) KW - Genetics KW - Molecular Biology KW - Ecology KW - Evolution KW - Behavior and Systematics SN - 1553-7404 TI - Dynamic association of NUP98 with the human genome VL - 9 ER - TY - JOUR AB - Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process. AU - Toyama, Brandon H. AU - Savas, Jeffrey N. AU - Park, Sung Kyu AU - Harris, Michael S. AU - Ingolia, Nicholas T. AU - Yates, John R. AU - HETZER, Martin W ID - 11087 IS - 5 JF - Cell KW - General Biochemistry KW - Genetics and Molecular Biology SN - 0092-8674 TI - Identification of long-lived proteins reveals exceptional stability of essential cellular structures VL - 154 ER - TY - JOUR AB - During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy. AU - Hatch, Emily M. AU - Fischer, Andrew H. AU - Deerinck, Thomas J. AU - HETZER, Martin W ID - 11085 IS - 1 JF - Cell KW - General Biochemistry KW - Genetics and Molecular Biology SN - 0092-8674 TI - Catastrophic nuclear envelope collapse in cancer cell micronuclei VL - 154 ER - TY - JOUR AB - The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM. AU - Regner, Benjamin M. AU - Vučinić, Dejan AU - Domnisoru, Cristina AU - Bartol, Thomas M. AU - HETZER, Martin W AU - Tartakovsky, Daniel M. AU - Sejnowski, Terrence J. ID - 11088 IS - 8 JF - Biophysical Journal KW - Biophysics SN - 0006-3495 TI - Anomalous diffusion of single particles in cytoplasm VL - 104 ER - TY - JOUR AB - Nuclear pore complex (NPC) proteins are known for their critical roles in regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope. However, recent findings suggest that some nucleoporins (Nups), including Nup98, have additional functions in developmental gene regulation. Nup98, which exhibits transcription-dependent mobility at the NPC but can also bind chromatin away from the nuclear envelope, is frequently involved in chromosomal translocations in a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm suggests that Nup98 translocations cause aberrant transcription when they are recuited to aberrant genomic loci. Importantly, this model fails to account for the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein levels to control transcription in healthy cells. In addition, we discuss the possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional activity of WT Nup98 in the nucleoplasm to drive AML. AU - Franks, Tobias M. AU - HETZER, Martin W ID - 11083 IS - 3 JF - Trends in Cell Biology KW - Cell Biology SN - 0962-8924 TI - The role of Nup98 in transcription regulation in healthy and diseased cells VL - 23 ER - TY - JOUR AB - Protein turnover is an effective way of maintaining a functional proteome, as old and potentially damaged polypeptides are destroyed and replaced by newly synthesized copies. An increasing number of intracellular proteins, however, have been identified that evade this turnover process and instead are maintained over a cell's lifetime. This diverse group of long-lived proteins might be particularly prone to accumulation of damage and thus have a crucial role in the functional deterioration of key regulatory processes during ageing. AU - Toyama, Brandon H. AU - HETZER, Martin W ID - 11084 JF - Nature Reviews Molecular Cell Biology KW - Cell Biology KW - Molecular Biology SN - 1471-0072 TI - Protein homeostasis: Live long, won't prosper VL - 14 ER - TY - JOUR AB - We present the design and performance characterization of a new experimental technique for measuring individual particle charges in large ensembles of macroscopic grains. The measurement principle is qualitatively similar to that used in determining the elementary charge by Millikan in that it follows individual particle trajectories. However, by taking advantage of new technology we are able to work with macroscopic grains and achieve several orders of magnitude better resolution in charge to mass ratios. By observing freely falling grains accelerated in a horizontal electric field with a co-falling, high-speed video camera, we dramatically increase particle tracking time and measurement precision. Keeping the granular medium under vacuum, we eliminate air drag, leaving the electrostatic force as the primary source of particle accelerations in the co-moving frame. Because the technique is based on direct imaging, we can distinguish between different particle types during the experiment, opening up the possibility of studying charge transfer processes between different particle species. For the ∼300 μm diameter grains reported here, we achieve an average acceleration resolution of ∼0.008 m/s2, a force resolution of ∼500 pN, and a median charge resolution ∼6× 104 elementary charges per grain (corresponding to surface charge densities ∼1 elementary charges per μm2). The primary source of error is indeterminacy in the grain mass, but with higher resolution cameras and better optics this can be further improved. The high degree of resolution and the ability to visually identify particles of different species or sizes with direct imaging make this a powerful new tool to characterize charging processes in granular media. AU - Waitukaitis, Scott R AU - Jaeger, Heinrich ID - 115 IS - 2 JF - Review of Scientific Instruments TI - In situ granular charge measurement by free-fall videography VL - 84 ER - TY - JOUR AB - We present the spatially resolved Hα dynamics of 16 star-forming galaxies at z ∼ 0.81 using the new KMOS multi-object integral field spectrograph on the ESO Very Large Telescope. These galaxies, selected using 1.18 μm narrowband imaging from the 10 deg2 CFHT-HiZELS survey of the SA 22 hr field, are found in a ∼4 Mpc overdensity of Hα emitters and likely reside in a group/intermediate environment, but not a cluster. We confirm and identify a rich group of star-forming galaxies at z = 0.813 ± 0.003, with 13 galaxies within 1000 km s−1 of each other, and seven within a diameter of 3 Mpc. All of our galaxies are “typical” star-forming galaxies at their redshift, 0.8 ± 0.4 SFR$^*_{z = 0.8}$, spanning a range of specific star formation rates (sSFRs) of 0.2–1.1 Gyr−1 and have a median metallicity very close to solar of 12 + log(O/H) = 8.62 ± 0.06. We measure the spatially resolved Hα dynamics of the galaxies in our sample and show that 13 out of 16 galaxies can be described by rotating disks and use the data to derive inclination corrected rotation speeds of 50–275 km s−1. The fraction of disks within our sample is 75% ± 8%, consistent with previous results based on Hubble Space Telescope morphologies of Hα-selected galaxies at z ∼ 1 and confirming that disks dominate the SFR density at z ∼ 1. Our Hα galaxies are well fitted by the z ∼ 1–2 Tully–Fisher (TF) relation, confirming the evolution seen in the zero point. Apart from having, on average, higher stellar masses and lower sSFRs, our group galaxies at z = 0.81 present the same mass–metallicity and TF relation as z ∼ 1 field galaxies and are all disk galaxies. AU - Sobral, D. AU - Swinbank, A. M. AU - Stott, J. P. AU - Matthee, Jorryt J AU - Bower, R. G. AU - Smail, Ian AU - Best, P. AU - Geach, J. E. AU - Sharples, R. M. ID - 11520 IS - 2 JF - The Astrophysical Journal KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - galaxies: evolution – galaxies KW - high-redshift – galaxies KW - starburst SN - 0004-637X TI - The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS VL - 779 ER - TY - JOUR AB - We describe a model experiment for dynamic jamming: a two-dimensional collection of initially unjammed disks that are forced into the jammed state by uniaxial compression via a rake. This leads to a stable densification front that travels ahead of the rake, leaving regions behind it jammed. Using disk conservation in conjunction with an upper limit to the packing fraction at jamming onset, we predict the front speed as a function of packing fraction and rake speed. However, we find that the jamming front has a finite width, a feature that cannot be explained by disk conservation alone. This width appears to diverge on approach to jamming, which suggests that it may be related to growing lengthscales encountered in other jamming studies. AU - Waitukaitis, Scott R AU - Roth, Leah AU - Vitelli, Vincenzo AU - Jaeger, Heinrich ID - 116 IS - 4 JF - EPL TI - Dynamic jamming fronts VL - 102 ER - TY - JOUR AB - Given only the URL of a Web page, can we identify its language? In this article we examine this question. URL-based language classification is useful when the content of the Web page is not available or downloading the content is a waste of bandwidth and time. We built URL-based language classifiers for English, German, French, Spanish, and Italian by applying a variety of algorithms and features. As algorithms we used machine learning algorithms which are widely applied for text classification and state-of-art algorithms for language identification of text. As features we used words, various sized n-grams, and custom-made features (our novel feature set). We compared our approaches with two baseline methods, namely classification by country code top-level domains and classification by IP addresses of the hosting Web servers. We trained and tested our classifiers in a 10-fold cross-validation setup on a dataset obtained from the Open Directory Project and from querying a commercial search engine. We obtained the lowest F1-measure for English (94) and the highest F1-measure for German (98) with the best performing classifiers. We also evaluated the performance of our methods: (i) on a set of Web pages written in Adobe Flash and (ii) as part of a language-focused crawler. In the first case, the content of the Web page is hard to extract and in the second page downloading pages of the “wrong” language constitutes a waste of bandwidth. In both settings the best classifiers have a high accuracy with an F1-measure between 95 (for English) and 98 (for Italian) for the Adobe Flash pages and a precision between 90 (for Italian) and 97 (for French) for the language-focused crawler. AU - Baykan, Eda AU - Weber, Ingmar AU - Henzinger, Monika H ID - 11671 IS - 1 JF - ACM Transactions on the Web KW - Computer Networks and Communications SN - 1559-1131 TI - A comprehensive study of techniques for URL-based web page language classification VL - 7 ER - TY - CONF AB - The packing arrangement of individual particles inside a granular material and the resulting response to applied stresses depend critically on particle-particle interactions. One aspect that recently received attention are nanoscale surface features of particles, which play an important role in determining the strength of cohesive van der Waals and capillary interactions and also affect tribo-charging of grains. We describe experiments on freely falling granular streams that can detect the contributions from all three of these forces. We show that it is possible to measure the charge of individual grains and build up distributions that are detailed enough to provide stringent tests of tribo-charging models currently available. A second aspect concerns particle shape. In this case steric interactions become important and new types of aggregate behavior can be expected when non-convex particle shapes are considered that can interlock or entangle. However, a general connection between the mechanical response of a granular material and the constituents\' shape remains unknown. This has made it infeasible to tackle the "inverse packing problem", namely to start from a given, desired behavior for the aggregate as a whole and then find the particle shape the produces it. We discuss a new approach, using concepts rooted in artificial evolution that provides a way to solve this inverse problem. This approach facilitates exploring the role of arbitrary particle geometry in jammed systems and invites the discovery and design of granular matter with optimized properties. AU - Jaeger, Heinrich AU - Miskin, Marc AU - Waitukaitis, Scott R ID - 117 T2 - AIP Conference Proceedings TI - From nanoscale cohesion to macroscale entanglement: opportunities for designing granular aggregate behaviour by tailoring grain shape and interactions VL - 1542 ER - TY - JOUR AB - Matching markets play a prominent role in economic theory. A prime example of such a market is the sponsored search market. Here, as in other markets of that kind, market equilibria correspond to feasible, envy free, and bidder optimal outcomes. For settings without budgets such an outcome always exists and can be computed in polynomial-time by the so-called Hungarian Method. Moreover, every mechanism that computes such an outcome is incentive compatible. We show that the Hungarian Method can be modified so that it finds a feasible, envy free, and bidder optimal outcome for settings with budgets. We also show that in settings with budgets no mechanism that computes such an outcome can be incentive compatible for all inputs. For inputs in general position, however, the presented mechanism—as any other mechanism that computes such an outcome for settings with budgets—is incentive compatible. AU - Dütting, Paul AU - Henzinger, Monika H AU - Weber, Ingmar ID - 11759 IS - 3 JF - Information Processing Letters SN - 0020-0190 TI - Sponsored search, market equilibria, and the Hungarian Method VL - 113 ER - TY - CONF AB - We study the problem of maintaining a breadth-first spanning tree (BFS tree) in partially dynamic distributed networks modeling a sequence of either failures or additions of communication links (but not both). We show (1 + ε)-approximation algorithms whose amortized time (over some number of link changes) is sublinear in D, the maximum diameter of the network. This breaks the Θ(D) time bound of recomputing “from scratch”. Our technique also leads to a (1 + ε)-approximate incremental algorithm for single-source shortest paths (SSSP) in the sequential (usual RAM) model. Prior to our work, the state of the art was the classic exact algorithm of [9] that is optimal under some assumptions [27]. Our result is the first to show that, in the incremental setting, this bound can be beaten in certain cases if a small approximation is allowed. AU - Henzinger, Monika H AU - Krinninger, Sebastian AU - Nanongkai, Danupon ID - 11793 SN - 1611-3349 T2 - 40th International Colloquium on Automata, Languages, and Programming TI - Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks VL - 7966 ER - TY - CONF AB - The focus of classic mechanism design has been on truthful direct-revelation mechanisms. In the context of combinatorial auctions the truthful direct-revelation mechanism that maximizes social welfare is the VCG mechanism. For many valuation spaces computing the allocation and payments of the VCG mechanism, however, is a computationally hard problem. We thus study the performance of the VCG mechanism when bidders are forced to choose bids from a subspace of the valuation space for which the VCG outcome can be computed efficiently. We prove improved upper bounds on the welfare loss for restrictions to additive bids and upper and lower bounds for restrictions to non-additive bids. These bounds show that the welfare loss increases in expressiveness. All our bounds apply to equilibrium concepts that can be computed in polynomial time as well as to learning outcomes. AU - Dütting, Paul AU - Henzinger, Monika H AU - Starnberger, Martin ID - 11791 SN - 1611-3349 T2 - 9th International Conference on Web and Internet Economics TI - Valuation compressions in VCG-based combinatorial auctions VL - 8289 ER - TY - CONF AB - We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the so-called food web, encoding viability constraints between these species. These food webs usually have constant depth. The goal is to select a subset of k species that satisfies the viability constraints and has maximal phylogenetic diversity. As this problem is known to be NP-hard, we investigate approximation algorithm. We present the first constant factor approximation algorithm if the depth is constant. Its approximation ratio is (1−1𝑒√). This algorithm not only applies to phylogenetic trees with viability constraints but for arbitrary monotone submodular set functions with viability constraints. Second, we show that there is no (1 − 1/e + ε)-approximation algorithm for our problem setting (even for additive functions) and that there is no approximation algorithm for a slight extension of this setting. AU - Dvořák, Wolfgang AU - Henzinger, Monika H AU - Williamson, David P. ID - 11792 SN - 1611-3349 T2 - 21st Annual European Symposium on Algorithms TI - Maximizing a submodular function with viability constraints VL - 8125 ER - TY - CONF AB - We study dynamic (1 + ϵ)-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected n-node m-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with a total update time of Ȏ(mn) and constant query time by Roditty and Zwick (FOCS 2004). The fastest deterministic algorithm is from a 1981 paper by Even and Shiloach (JACM 1981); it has a total update time of O(mn 2 ) and constant query time. We improve these results as follows: (1) We present an algorithm with a total update time of Ȏ(n 5/2 ) and constant query time that has an additive error of two in addition to the 1 + ϵ multiplicative error. This beats the previous Ȏ(mn) time when m = Ω(n 3/2 ). Note that the additive error is unavoidable since, even in the static case, an O(n 3-δ )-time (a so-called truly sub cubic) combinatorial algorithm with 1 + ϵ multiplicative error cannot have an additive error less than 2 - ϵ, unless we make a major breakthrough for Boolean matrix multiplication (Dor, Halperin and Zwick FOCS 1996) and many other long-standing problems (Vassilevska Williams and Williams FOCS 2010). The algorithm can also be turned into a (2 + ϵ)-approximation algorithm (without an additive error) with the same time guarantees, improving the recent (3 + ϵ)-approximation algorithm with Ȏ(n 5/2+O(1√(log n)) ) running time of Bernstein and Roditty (SODA 2011) in terms of both approximation and time guarantees. (2) We present a deterministic algorithm with a total update time of Ȏ(mn) and a query time of O(log log n). The algorithm has a multiplicative error of 1 + ϵ and gives the first improved deterministic algorithm since 1981. It also answers an open question raised by Bernstein in his STOC 2013 paper. In order to achieve our results, we introduce two new techniques: (1) A lazy Even-Shiloach tree algorithm which maintains a bounded-distance shortest-paths tree on a certain type of emulator called locally persevering emulator. (2) A derandomization technique based on moving Even-Shiloach trees as a way to derandomize the standard random set argument. These techniques might be of independent interest. AU - Henzinger, Monika H AU - Krinninger, Sebastian AU - Nanongkai, Danupon ID - 11856 SN - 0272-5428 T2 - 54th Annual Symposium on Foundations of Computer Science TI - Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization ER - TY - JOUR AB - We study the problem of matching bidders to items where each bidder i has general, strictly monotonic utility functions ui,j(pj) expressing his utility of being matched to item j at price pj. For this setting we prove that a bidder optimal outcome always exists, even when the utility functions are non-linear and non-continuous. We give sufficient conditions under which every mechanism that finds a bidder optimal outcome is incentive compatible. We also give a mechanism that finds a bidder optimal outcome if the conditions for incentive compatibility are satisfied. The running time of this mechanism is exponential in the number of items, but polynomial in the number of bidders. AU - Dütting, Paul AU - Henzinger, Monika H AU - Weber, Ingmar ID - 11902 IS - 3 JF - Theoretical Computer Science SN - 0304-3975 TI - Bidder optimal assignments for general utilities VL - 478 ER - TY - JOUR AB - No catalyst required! A highly efficient, catalyst-free process to generate diimide in situ from hydrazine monohydrate and molecular oxygen for the selective reduction of alkenes has been developed. The use of a gas–liquid segmented flow system allowed safe operating conditions and dramatically enhanced this atom-economical reaction, resulting in short processing times. AU - Pieber, Bartholomäus AU - Martinez, Sabrina Teixeira AU - Cantillo, David AU - Kappe, C. Oliver ID - 11959 IS - 39 JF - Angewandte Chemie International Edition SN - 1433-7851 TI - In situ generation of diimide from hydrazine and oxygen: Continuous-flow transfer hydrogenation of olefins VL - 52 ER - TY - JOUR AB - It's not magic! The effects observed in microwave-irradiated chemical transformations can in most cases be rationalized by purely bulk thermal phenomena associated with rapid heating to elevated temperatures. As discussed in this Essay, the existence of so-called nonthermal or specific microwave effects is highly doubtful. AU - Kappe, C. Oliver AU - Pieber, Bartholomäus AU - Dallinger, Doris ID - 11960 IS - 4 JF - Angewandte Chemie International Edition SN - 1433-7851 TI - Microwave effects in organic synthesis: Myth or reality? VL - 52 ER - TY - JOUR AB - The use of high-temperature/pressure gas–liquid continuous flow conditions dramatically enhances the iron-catalyzed aerobic oxidation of 2-benzylpyridines to their corresponding ketones. Pressurized air serves as a readily available oxygen source and propylene carbonate as a green solvent in this radically intensified preparation of synthetically valuable 2-aroylpyridines. AU - Pieber, Bartholomäus AU - Kappe, C. Oliver ID - 11973 IS - 2 JF - Green Chemistry SN - 1463-9262 TI - Direct aerobic oxidation of 2-benzylpyridines in a gas-liquid continuous-flow regime using propylene carbonate as a solvent VL - 15 ER - TY - JOUR AB - Near-surface air temperature, typically measured at a height of 2 m, is the most important control on the energy exchange and the melt rate at a snow or ice surface. It is distributed in a simplistic manner in most glacier melt models by using constant linear lapse rates, which poorly represent the actual spatial and temporal variability of air temperature. In this paper, we test a simple thermodynamic model proposed by Greuell and Böhm in 1998 as an alternative, using a new dataset of air temperature measurements from along the flowline of Haut Glacier d’Arolla, Switzerland. The unmodified model performs little better than assuming a constant linear lapse rate. When modified to allow the ratio of the boundary layer height to the bulk heat transfer coefficient to vary along the flowline, the model matches measured air temperatures better, and a further reduction of the root-mean-square error is obtained, although there is still considerable scope for improvement. The modified model is shown to perform best under conditions favourable to the development of katabatic winds – few clouds, positive ambient air temperature, limited influence of synoptic or valley winds and a long fetch – but its performance is poor under cloudy conditions. AU - Petersen, Lene AU - Pellicciotti, Francesca AU - Juszak, Inge AU - Carenzo, Marco AU - Brock, Ben ID - 12642 IS - 63 JF - Annals of Glaciology KW - Earth-Surface Processes SN - 0260-3055 TI - Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative VL - 54 ER - TY - JOUR AB - Parameterizations of incoming longwave radiation are increasingly receiving attention for both low and high elevation glacierized sites. In this paper, we test 13 clear-sky parameterizations combined with seven cloud corrections for all-sky atmospheric emissivity at one location on Haut Glacier d'Arolla. We also analyze the four seasons separately and conduct a cross-validation to test the parameters’ robustness. The best parameterization is the one by Dilley and O'Brien, B for clear-sky conditions combined with Unsworth and Monteith cloud correction. This model is also the most robust when tested in cross-validation. When validated at different sites in the southern Alps of Switzerland and north-western Italian Alps, all parameterizations show a substantial decrease in performance, except for one site, thus suggesting that it is important to recalibrate parameterizations of incoming longwave radiation for different locations. We argue that this is due to differences in the structure of the atmosphere at the sites. We also quantify the effect that the incoming longwave radiation parameterizations have on energy-balance melt modeling, and show that recalibration of model parameters is needed. Using parameters from other sites leads to a significant underestimation of melt and to an error that is larger than that associated with using different parameterizations. Once recalibrated, however, the parameters of most models seem to be stable over seasons and years at the location on Haut Glacier d'Arolla. AU - Juszak, I. AU - Pellicciotti, Francesca ID - 12643 IS - 8 JF - Journal of Geophysical Research: Atmospheres KW - Space and Planetary Science KW - Earth and Planetary Sciences (miscellaneous) KW - Atmospheric Science KW - Geophysics SN - 2169-897X TI - A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability VL - 118 ER - TY - JOUR AB - Greater Himalayan glaciers are retreating and losing mass at rates comparable to glaciers in other regions of the world1,2,3,4,5. Assessments of future changes and their associated hydrological impacts are scarce, oversimplify glacier dynamics or include a limited number of climate models6,7,8,9. Here, we use results from the latest ensemble of climate models in combination with a high-resolution glacio-hydrological model to assess the hydrological impact of climate change on two climatically contrasting watersheds in the Greater Himalaya, the Baltoro and Langtang watersheds that drain into the Indus and Ganges rivers, respectively. We show that the largest uncertainty in future runoff is a result of variations in projected precipitation between climate models. In both watersheds, strong, but highly variable, increases in future runoff are projected and, despite the different characteristics of the watersheds, their responses are surprisingly similar. In both cases, glaciers will recede but net glacier melt runoff is on a rising limb at least until 2050. In combination with a positive change in precipitation, water availability during this century is not likely to decline. We conclude that river basins that depend on monsoon rains and glacier melt will continue to sustain the increasing water demands expected in these areas10. AU - Immerzeel, W. W. AU - Pellicciotti, Francesca AU - Bierkens, M. F. P. ID - 12640 IS - 9 JF - Nature Geoscience KW - General Earth and Planetary Sciences SN - 1752-0894 TI - Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds VL - 6 ER - TY - JOUR AB - We investigate the sensitivity of a distributed enhanced temperature-index (ETI) melt model, in order to understand which parameters have the largest influence on model outputs and thus need to be accurately known. We use melt and meteorological data from two Alpine glaciers and one glacier in the Andes of Chile. Sensitivity analysis is conducted in a systematic way in terms of parameters and the different conditions (day, night, clear-sky, overcast), melt seasons and glaciers examined. The sensitivity of total melt to changes in individual parameters is calculated using a local method around the optimal value of the parameters. We verify that the parameters are optimal at the distributed scale and assess the model uncertainty induced by uncertainty in the parameters using a Monte Carlo technique. Model sensitivity to parameters is consistent across melt seasons, glaciers, different conditions and the daily statistics examined. The parameters to which the model is most sensitive are the shortwave-radiation factor, the temperature lapse rate for extrapolation of air temperature, the albedo parameters, the temperature threshold and the cloud transmittance factor parameters. A parameter uncertainty of 5% results in a model uncertainty of 5.6% of mean melt on Haut Glacier d’Arolla, Switzerland. AU - Heynen, Martin AU - Pellicciotti, Francesca AU - Carenzo, Marco ID - 12641 IS - 63 JF - Annals of Glaciology SN - 0260-3055 TI - Parameter sensitivity of a distributed enhanced temperature-index melt model VL - 54 ER - TY - JOUR AB - When confronted with a large-field stimulus rotating around the vertical body axis, flies display a following behavior called "optomotor response." As neural control elements, the large tangential horizontal system (HS) cells of the lobula plate have been prime candidates for long. Here, we applied optogenetic stimulation of HS cells to evaluate their behavioral role in Drosophila. To minimize interference of the optical activation of channelrhodopsin-2 with the visual perception of the flies, we used a bistable variant called ChR2-C128S. By applying pulses of blue and yellow light, we first demonstrate electrophysiologically that lobula plate tangential cells can be activated and deactivated repeatedly with no evident change in depolarization strength over trials. We next show that selective optogenetic activation of HS cells elicits robust yaw head movements and yaw turning responses in fixed and tethered flying flies, respectively. AU - Haikala, Väinö AU - Maximilian Jösch AU - Borst, Alexander AU - Mauss, Alex S ID - 1304 IS - 34 JF - Journal of Neuroscience TI - Optogenetic control of fly optomotor responses VL - 33 ER - TY - JOUR AB - In the fly Drosophila melanogaster, photoreceptor input to motion vision is split into two parallel pathways as represented by first-order interneurons L1 and L2 (Rister et al., 2007; Joesch et al., 2010). However, how these pathways are functionally specialized remains controversial. One study (Eichner et al., 2011) proposed that the L1-pathway evaluates only sequences of brightness increments (ON-ON), while the L2-pathway processes exclusively brightness decrements (OFF-OFF). Another study (Clark et al., 2011) proposed that each of the two pathways evaluates both ON-ON and OFF-OFF sequences. To decide between these alternatives, we recorded from motionsensitive neurons in flies in which the output from either L1 or L2 was genetically blocked. We found that blocking L1 abolishes ON-ON responses but leaves OFF-OFF responses intact. The opposite was true, when the output from L2 was blocked. We conclude that the L1 and L2 pathways are functionally specialized to detect ON-ON and OFF-OFF sequences, respectively. AU - Maximilian Jösch AU - Weber, Franz AU - Eichner, Hubert AU - Borst, Alexander ID - 1305 IS - 3 JF - Journal of Neuroscience TI - Functional specialization of parallel motion detection circuits in the fly VL - 33 ER - TY - JOUR AB - We derive sufficient conditions for advection-driven backward motion of the free boundary in a chemotaxis model with degenerate mobility. In this model, a porous-medium-type diffusive term and an advection term are in competition. The former induces forward motion, the latter may induce backward motion of the free boundary depending on the direction of advection. We deduce conditions on the growth of the initial data at the free boundary which ensure that at least initially the advection term is dominant. This implies local backward motion of the free boundary provided the advection is (locally) directed appropriately. Our result is based on a new class of moving test functions and Stampacchia's lemma. As a by-product of our estimates, we obtain quantitative bounds on the spreading of the support of solutions for the chemotaxis model and provide a proof for the finite speed of the support propagation property of solutions. AU - Julian Fischer ID - 1308 IS - 3 JF - SIAM Journal on Mathematical Analysis TI - Advection-driven support shrinking in a chemotaxis model with degenerate mobility VL - 45 ER - TY - JOUR AB - We prove uniqueness of solutions of the DLSS equation in a class of sufficiently regular functions. The global weak solutions of the DLSS equation constructed by Jüngel and Matthes belong to this class of uniqueness. We also show uniqueness of solutions for the quantum drift-diffusion equation, which contains additional drift and second-order diffusion terms. The results hold in case of periodic or Dirichlet-Neumann boundary conditions. Our proof is based on a monotonicity property of the DLSS operator and sophisticated approximation arguments; we derive a PDE satisfied by the pointwise square root of the solution, which enables us to exploit the monotonicity property of the operator. AU - Julian Fischer ID - 1307 IS - 11 JF - Communications in Partial Differential Equations TI - Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models VL - 38 ER - TY - JOUR AB - We derive lower bounds on asymptotic support propagation rates for strong solutions of the Cauchy problem for the thin-film equation. The bounds coincide up to a constant factor with the previously known upper bounds and thus are sharp. Our results hold in case of at most three spatial dimensions and n∈. (1, 2.92). The result is established using weighted backward entropy inequalities with singular weight functions to yield a differential inequality; combined with some entropy production estimates, the optimal rate of propagation is obtained. To the best of our knowledge, these are the first lower bounds on asymptotic support propagation rates for higher-order nonnegativity-preserving parabolic equations. AU - Julian Fischer ID - 1310 IS - 10 JF - Journal of Differential Equations TI - Optimal lower bounds on asymptotic support propagation rates for the thin-film equation VL - 255 ER - TY - CONF AB - We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete. AU - Chatterjee, Krishnendu AU - Fijalkow, Nathanaël ID - 1374 T2 - 22nd EACSL Annual Conference on Computer Science Logic TI - Infinite-state games with finitary conditions VL - 23 ER - TY - CONF AB - It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results. AU - Hofferek, Georg AU - Gupta, Ashutosh AU - Könighofer, Bettina AU - Jiang, Jie AU - Bloem, Roderick ID - 1385 T2 - 2013 Formal Methods in Computer-Aided Design TI - Synthesizing multiple boolean functions using interpolation on a single proof ER - TY - CONF AB - Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata. AU - Boker, Udi AU - Kuperberg, Denis AU - Kupferman, Orna AU - Skrzypczak, Michał ID - 1387 IS - PART 2 TI - Nondeterminism in the presence of a diverse or unknown future VL - 7966 ER - TY - JOUR AB - We give a cohomological interpretation of both the Kac polynomial and the refined Donaldson-Thomas-invariants of quivers. This interpretation yields a proof of a conjecture of Kac from 1982 and gives a new perspective on recent work of Kontsevich-Soibelman. Thisis achieved by computing, via an arithmetic Fourier transform, the dimensions of the isotypical components of the cohomology of associated Nakajima quiver varieties under the action of a Weyl group. The generating function of the corresponding Poincare polynomials is an extension of Hua's formula for Kac polynomials of quivers involving Hall-Littlewood symmetric functions. The resulting formulae contain a wide range of information on the geometry of the quiver varieties. AU - Tamas Hausel AU - Letellier, Emmanuel AU - Rodríguez Villegas, Fernando ID - 1442 IS - 3 JF - Annals of Mathematics TI - Positivity for Kac polynomials and DT-invariants of quivers VL - 177 ER - TY - CHAP AB - Here we survey several results and conjectures on the cohomology of the total space of the Hitchin system: the moduli space of semi-stable rank n and degree d Higgs bundles on a complex algebraic curve C. The picture emerging is a dynamic mixture of ideas originating in theoretical physics such as gauge theory and mirror symmetry, Weil conjectures in arithmetic algebraic geometry, representation theory of finite groups of Lie type and Langlands duality in number theory. AU - Tamas Hausel ID - 1443 T2 - Handbook of Moduli: Volume II TI - Global topology of the Hitchin system VL - 25 ER - TY - JOUR AB - We study connections between the topology of generic character varieties of fundamental groups of punctured Riemann surfaces, Macdonald polynomials, quiver representations, Hilbert schemes on Cx × Cx, modular forms and multiplicities in tensor products of irreducible characters of finite general linear groups. AU - Tamas Hausel AU - Letellier, Emmanuel AU - Rodríguez Villegas, Fernando ID - 1469 JF - Advances in Mathematics TI - Arithmetic harmonic analysis on character and quiver varieties II VL - 234 ER - TY - JOUR AB - We show that a natural isomorphism between the rational cohomology groups of the two zero-dimensional Hilbert schemes of n-points of two surfaces, the affine plane minus the axes and the cotangent bundle of an elliptic curve, exchanges the weight filtration on the first set of cohomology groups with the perverse Leray filtration associated with a natural fibration on the second set of cohomology groups. We discuss some associated hard Lefschetz phenomena. AU - De Cataldo, Mark A AU - Tamas Hausel AU - Migliorini, Luca ID - 1470 JF - Journal of Singularities TI - Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces VL - 7 ER - TY - JOUR AU - Aceto, Luca AU - Henzinger, Monika H AU - Sgall, Jiří ID - 11758 IS - 1 JF - Information and Computation SN - 0890-5401 TI - 38th International Colloquium on Automata, Languages and Programming VL - 222 ER - TY - JOUR AB - The development of a functional tissue requires coordination of the amplification of progenitors and their differentiation into specific cell types. The molecular basis for this coordination during myotome ontogeny is not well understood. Dermomytome progenitors that colonize the myotome first acquire myocyte identity and subsequently proliferate as Pax7-expressing progenitors before undergoing terminal differentiation. We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this transition in both avian and mouse embryos. Initially, Shh ligand emanating from notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation of dermomyotome cells and promotes myogenic differentiation of progenitors that colonized the myotome. Interfering with Shh signaling at this stage produces small myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter of Shh activity combined with mouse genetics revealed the existence of both activator and repressor Shh activities operating on distinct subsets of cells during the epaxial myotomal maturation. In contrast to observations in mice, in avians Shh promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently, myogenic progenitors become refractory to Shh; this is likely to occur at the level of, or upstream of, smoothened signaling. The end of responsiveness to Shh coincides with, and is thus likely to enable, the transition into the growth phase of the myotome. AU - Kahane, Nitza AU - Ribes, Vanessa AU - Anna Kicheva AU - Briscoe, James AU - Kalcheim, Chaya ID - 1726 IS - 8 JF - Development TI - The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling VL - 140 ER - TY - JOUR AB - Cells at different positions in a developing tissue receive different concentrations of signaling molecules, called morphogens, and this influences their cell fate. Morphogen concentration gradients have been proposed to control patterning as well as growth in many developing tissues. Some outstanding questions about tissue patterning by morphogen gradients are the following: What are the mechanisms that regulate gradient formation and shape? Is the positional information encoded in the gradient sufficiently precise to determine the positions of target gene domain boundaries? What are the temporal dynamics of gradients and how do they relate to patterning and growth? These questions are inherently quantitative in nature and addressing them requires measuring morphogen concentrations in cells, levels of downstream signaling activity, and kinetics of morphogen transport. Here we first present methods for quantifying morphogen gradient shape in which the measurements can be calibrated to reflect actual morphogen concentrations. We then discuss using fluorescence recovery after photobleaching to study the kinetics of morphogen transport at the tissue level. Finally, we present particle tracking as a method to study morphogen intracellular trafficking. AU - Anna Kicheva AU - Holtzer, Laurent AU - Wartlick, Ortrud AU - Schmidt, Thomas S AU - González-Gaitán, Marcos A ID - 1727 IS - 5 JF - Cold Spring Harbor Protocols TI - Quantitative imaging of morphogen gradients in drosophila imaginal discs VL - 8 ER - TY - JOUR AB - We report on hole g-factor measurements in three terminal SiGe self-assembled quantum dot devices with a top gate electrode positioned very close to the nanostructure. Measurements of both the perpendicular as well as the parallel g-factor reveal significant changes for a small modulation of the top gate voltage. From the observed modulations, we estimate that, for realistic experimental conditions, hole spins can be electrically manipulated with Rabi frequencies in the order of 100 MHz. This work emphasises the potential of hole-based nano-devices for efficient spin manipulation by means of the g-tensor modulation technique. AU - Ares, Natalia AU - Georgios Katsaros AU - Golovach, Vitaly N AU - Zhang, Jianjun AU - Prager, Aaron A AU - Glazman, Leonid I AU - Schmidt, Oliver G AU - De Franceschi, Silvano ID - 1760 IS - 26 JF - Applied Physics Letters TI - SiGe quantum dots for fast hole spin Rabi oscillations VL - 103 ER - TY - JOUR AB - We report an electric-field-induced giant modulation of the hole g factor in SiGe nanocrystals. The observed effect is ascribed to a so-far overlooked contribution to the g factor that stems from the mixing between heavy- and light-hole wave functions. We show that the relative displacement between the confined heavy- and light-hole states, occurring upon application of the electric field, alters their mixing strength leading to a strong nonmonotonic modulation of the g factor. AU - Ares, Natalia AU - Golovach, Vitaly N AU - Georgios Katsaros AU - Stoffel, Mathieu AU - Fournel, Frank AU - Glazman, Leonid I AU - Schmidt, Oliver G AU - De Franceschi, Silvano ID - 1759 IS - 4 JF - Physical Review Letters TI - Nature of tunable hole g factors in quantum dots VL - 110 ER - TY - JOUR AB - The geometric aspects of quantum mechanics are emphasized most prominently by the concept of geometric phases, which are acquired whenever a quantum system evolves along a path in Hilbert space, that is, the space of quantum states of the system. The geometric phase is determined only by the shape of this path and is, in its simplest form, a real number. However, if the system has degenerate energy levels, then matrix-valued geometric state transformations, known as non-Abelian holonomies-the effect of which depends on the order of two consecutive paths-can be obtained. They are important, for example, for the creation of synthetic gauge fields in cold atomic gases or the description of non-Abelian anyon statistics. Moreover, there are proposals to exploit non-Abelian holonomic gates for the purposes of noise-resilient quantum computation. In contrast to Abelian geometric operations, non-Abelian ones have been observed only in nuclear quadrupole resonance experiments with a large number of spins, and without full characterization of the geometric process and its non-commutative nature. Here we realize non-Abelian non-adiabatic holonomic quantum operations on a single, superconducting, artificial three-level atom by applying a well-controlled, two-tone microwave drive. Using quantum process tomography, we determine fidelities of the resulting non-commuting gates that exceed 95 per cent. We show that two different quantum gates, originating from two distinct paths in Hilbert space, yield non-equivalent transformations when applied in different orders. This provides evidence for the non-Abelian character of the implemented holonomic quantum operations. In combination with a non-trivial two-quantum-bit gate, our method suggests a way to universal holonomic quantum computing. AU - Abdumalikov, Abdufarrukh A AU - Johannes Fink AU - Juliusson, K AU - Pechal, M AU - Berger, Stefan T AU - Wallraff, Andreas AU - Filipp, Stefan ID - 1785 IS - 7446 JF - Nature TI - Experimental realization of non-Abelian non-adiabatic geometric gates VL - 496 ER - TY - JOUR AB - When two indistinguishable single photons impinge at the two inputs of a beam splitter they coalesce into a pair of photons appearing in either one of its two outputs. This effect is due to the bosonic nature of photons and was first experimentally observed by Hong, Ou and Mandel. Here, we present the observation of the Hong-Ou-Mandel effect with two independent single-photon sources in the microwave frequency domain. We probe the indistinguishability of single photons, created with a controllable delay, in time-resolved second-order cross- and auto-correlation function measurements. Using quadrature amplitude detection we are able to resolve different photon numbers and detect coherence in and between the output arms. This scheme allows us to fully characterize the two-mode entanglement of the spatially separated beam-splitter output modes. Our experiments constitute a first step towards using two-photon interference at microwave frequencies for quantum communication and information processing. AU - Lang, C AU - Eichler, Christopher AU - Steffen, L. Kraig AU - Johannes Fink AU - Woolley, Matthew J AU - Blais, Alexandre AU - Wallraff, Andreas ID - 1787 IS - 6 JF - Nature Physics TI - Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies VL - 9 ER - TY - JOUR AB - We report the experimental observation and a theoretical explanation of collective suppression of linewidths for multiple superconducting qubits coupled to a good cavity. This demonstrates how strong qubit-cavity coupling can significantly modify the dephasing and dissipation processes that might be expected for individual qubits, and can potentially improve coherence times in many-body circuit QED. AU - Nissen, Felix AU - Johannes Fink AU - Mlynek, Jonas A AU - Wallraff, Andreas AU - Keeling, Jonathan M ID - 1786 IS - 20 JF - Physical Review Letters TI - Collective suppression of linewidths in circuit QED VL - 110 ER - TY - JOUR AB - In the September 12, 2013 issue of Nature, the Epi4K Consortium (. Allen etal., 2013) reported sequencing 264patient trios with epileptic encephalopathies. The Consortium focused on genes exceptionally intolerant to sequence variations and found substantial interconnections with autism and intellectual disability gene networks. AU - Gaia Novarino AU - Baek, SeungTae AU - Gleeson, Joseph G ID - 1790 IS - 1 JF - Neuron TI - The sacred disease: The puzzling genetics of epileptic disorders VL - 80 ER - TY - JOUR AB - Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production, being the first and largest enzyme of the respiratory chain in mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative disorders. Mammalian complex I is composed of 44 different subunits, whereas the 'minimal' bacterial version contains 14 highly conserved 'core' subunits. The L-shaped assembly consists of hydrophilic and membrane domains. We have determined all known atomic structures of complex I, starting from the hydrophilic domain of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes, and finally culminating in a recent crystal structure of the entire intact complex I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane helices). The structure suggests an unusual and unique coupling mechanism via longrange conformational changes. Determination of the structure of the entire complex was possible only through this step-by-step approach, building on from smaller subcomplexes towards the entire assembly. Large membrane proteins are notoriously difficult to crystallize, and so various non-standard and sometimes counterintuitive approaches were employed in order to achieve crystal diffraction to high resolution and solve the structures. These steps, as well as the implications from the final structure, are discussed in the present review. AU - Leonid Sazanov AU - Baradaran, Rozbeh AU - Efremov, Rouslan G AU - Berrisford, John M AU - Minhas, Gurdeep S ID - 1977 IS - 5 JF - Biochemical Society Transactions TI - A long road towards the structure of respiratory complex I, a giant molecular proton pump VL - 41 ER - TY - JOUR AB - Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle. AU - Baradaran, Rozbeh AU - Berrisford, John M AU - Minhas, Gurdeep S AU - Leonid Sazanov ID - 1978 IS - 7438 JF - Nature TI - Crystal structure of the entire respiratory complex i VL - 494 ER - TY - JOUR AB - Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome-specific adaptations such as dosage compensation or an accumulation of sex-specific mutations. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination or its targeting by a chromosome-specific regulatory mechanism. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur. AU - Beatriz Vicoso AU - Bachtrog, Doris ID - 1991 IS - 7458 JF - Nature TI - Reversal of an ancient sex chromosome to an autosome in Drosophila VL - 499 ER - TY - JOUR AB - The rod-shaped bacterium Escherichia coli selects the cell center as site of division with the help of the proteins MinC, MinD, and MinE. This protein system collectively oscillates between the two cell poles by alternately binding to the membrane in one of the two cell halves. This dynamic behavior, which emerges from the interaction of the ATPase MinD and its activator MinE on the cell membrane, has become a paradigm for protein self-organization. Recently, it has been found that not only the binding of MinD to the membrane, but also interactions of MinE with the membrane contribute to Min-protein self-organization. Here, we show that by accounting for this finding in a computational model, we can comprehensively describe all observed Min-protein patterns in vivo and in vitro. Furthermore, by varying the system's geometry, our computations predict patterns that have not yet been reported. We confirm these predictions experimentally. AU - Bonny, Mike AU - Fischer-Friedrich, Elisabeth AU - Martin Loose AU - Schwille, Petra AU - Kruse, Karsten ID - 1988 IS - 12 JF - PLoS Computational Biology TI - Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation VL - 9 ER - TY - JOUR AB - Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case. AU - Uhler, Caroline AU - Raskutti, Garvesh AU - Bühlmann, Peter AU - Yu, Bin ID - 2010 IS - 2 JF - The Annals of Statistics TI - Geometry of the faithfulness assumption in causal inference VL - 41 ER - TY - JOUR AB - Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression. AU - Uhler, Caroline AU - Slavkovic, Aleksandra AU - Fienberg, Stephen ID - 2009 IS - 1 JF - Journal of Privacy and Confidentiality TI - Privacy-preserving data sharing for genome-wide association studies VL - 5 ER - TY - JOUR AB - Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. AU - Beatriz Vicoso AU - Kaiser, Vera B AU - Bachtrog, Doris ID - 2074 IS - 16 JF - PNAS TI - Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution VL - 110 ER -