@article{1492,
abstract = {To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated cells with a preserved prolif eration capacity. The root pericycle represents a unique tissue with conditional meristematic activity, and its tight control determines initiation of lateral organs. Here we show that the meristematic activity of the pericycle is constrained by the interaction with the adjacent endodermis. Release of these restraints by elimination of endo dermal cells by single-cell ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis removal substitutes for the phytohormone auxin-dependent initiation of the pericycle meristematic activity. However, auxin is indispensable to steer the cell division plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally distinct role for auxin during lateral root initiation. In the endodermis, auxin releases constraints arising from cell-to-cell interactions that compromise the pericycle meristematic activity, whereas, in the pericycle, auxin defines the orientation of the cell division plane to initiate lateral roots.},
author = {Marhavy, Peter and Montesinos López, Juan C and Abuzeineh, Anas and Van Damme, Daniël and Vermeer, Joop and Duclercq, Jérôme and Rakusova, Hana and Marhavá, Petra and Friml, Jirí and Geldner, Niko and Benková, Eva},
journal = {Genes and Development},
number = {4},
pages = {471 -- 483},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation}},
doi = {10.1101/gad.276964.115},
volume = {30},
year = {2016},
}
@article{1493,
abstract = {We introduce a new method for deriving the time-dependent Hartree or Hartree-Fock equations as an effective mean-field dynamics from the microscopic Schrödinger equation for fermionic many-particle systems in quantum mechanics. The method is an adaption of the method used in Pickl (Lett. Math. Phys. 97 (2) 151–164 2011) for bosonic systems to fermionic systems. It is based on a Gronwall type estimate for a suitable measure of distance between the microscopic solution and an antisymmetrized product state. We use this method to treat a new mean-field limit for fermions with long-range interactions in a large volume. Some of our results hold for singular attractive or repulsive interactions. We can also treat Coulomb interaction assuming either a mild singularity cutoff or certain regularity conditions on the solutions to the Hartree(-Fock) equations. In the considered limit, the kinetic and interaction energy are of the same order, while the average force is subleading. For some interactions, we prove that the Hartree(-Fock) dynamics is a more accurate approximation than a simpler dynamics that one would expect from the subleading force. With our method we also treat the mean-field limit coupled to a semiclassical limit, which was discussed in the literature before, and we recover some of the previous results. All results hold for initial data close (but not necessarily equal) to antisymmetrized product states and we always provide explicit rates of convergence.},
author = {Petrat, Sören P and Pickl, Peter},
journal = {Mathematical Physics, Analysis and Geometry},
number = {1},
publisher = {Springer},
title = {{A new method and a new scaling for deriving fermionic mean-field dynamics}},
doi = {10.1007/s11040-016-9204-2},
volume = {19},
year = {2016},
}
@article{1496,
abstract = {The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is theoretically investigated within a fully relativistic framework and a second-order perturbation theory. We focus our analysis on how electron correlation, as well as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For this purpose, we include the electronic correlation via an effective local potential and within a single configuration-state model. Due to its experimental interest, evaluations of decay rates are performed for berylliumlike xenon and uranium. We find that the negative-energy contribution can be neglected at the present level of accuracy in the evaluation of the decay rate. On the other hand, if contributions of electronic correlation are not carefully taken into account, it may change the lifetime of the metastable state by up to 20%. By performing a full-relativistic jj-coupling calculation, we found a decrease of the decay rate by two orders of magnitude compared to non-relativistic LS-coupling calculations, for the selected heavy ions.},
author = {Amaro, Pedro and Fratini, Filippo and Safari, Laleh and Machado, Jorge and Guerra, Mauro and Indelicato, Paul and Santos, José},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {3},
publisher = {American Physical Society},
title = {{Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model}},
doi = {10.1103/PhysRevA.93.032502},
volume = {93},
year = {2016},
}
@article{1545,
abstract = {We provide general conditions for which bosonic quadratic Hamiltonians on Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover the case when quantum systems have infinite degrees of freedom and the associated one-body kinetic and paring operators are unbounded. Our sufficient conditions are optimal in the sense that they become necessary when the relevant one-body operators commute.},
author = {Nam, Phan and Napiórkowski, Marcin M and Solovej, Jan},
journal = {Journal of Functional Analysis},
number = {11},
pages = {4340 -- 4368},
publisher = {Academic Press},
title = {{Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations}},
doi = {10.1016/j.jfa.2015.12.007},
volume = {270},
year = {2016},
}
@article{1552,
abstract = {Antibiotic resistance carries a fitness cost that must be overcome in order for resistance to persist over the long term. Compensatory mutations that recover the functional defects associated with resistance mutations have been argued to play a key role in overcoming the cost of resistance, but compensatory mutations are expected to be rare relative to generally beneficial mutations that increase fitness, irrespective of antibiotic resistance. Given this asymmetry, population genetics theory predicts that populations should adapt by compensatory mutations when the cost of resistance is large, whereas generally beneficial mutations should drive adaptation when the cost of resistance is small. We tested this prediction by determining the genomic mechanisms underpinning adaptation to antibiotic-free conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that carry costly antibiotic resistance mutations. Whole-genome sequencing revealed that populations founded by high-cost rifampicin-resistant mutants adapted via compensatory mutations in three genes of the RNA polymerase core enzyme, whereas populations founded by low-cost mutants adapted by generally beneficial mutations, predominantly in the quorum-sensing transcriptional regulator gene lasR. Even though the importance of compensatory evolution in maintaining resistance has been widely recognized, our study shows that the roles of general adaptation in maintaining resistance should not be underestimated and highlights the need to understand how selection at other sites in the genome influences the dynamics of resistance alleles in clinical settings.},
author = {Qi, Qin and Toll Riera, Macarena and Heilbron, Karl and Preston, Gail and Maclean, R Craig},
journal = {Proceedings of the Royal Society of London Series B Biological Sciences},
number = {1822},
publisher = {Royal Society, The},
title = {{The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa}},
doi = {10.1098/rspb.2015.2452},
volume = {283},
year = {2016},
}
@article{1408,
abstract = {The concept of well group in a special but important case captures homological properties of the zero set of a continuous map (Formula presented.) on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within (Formula presented.) distance r from f for a given (Formula presented.). The main drawback of the approach is that the computability of well groups was shown only when (Formula presented.) or (Formula presented.). Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of (Formula presented.) by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and (Formula presented.), our approximation of the (Formula presented.)th well group is exact. For the second part, we find examples of maps (Formula presented.) with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status.},
author = {Franek, Peter and Krcál, Marek},
journal = {Discrete & Computational Geometry},
number = {1},
pages = {126 -- 164},
publisher = {Springer},
title = {{On computability and triviality of well groups}},
doi = {10.1007/s00454-016-9794-2},
volume = {56},
year = {2016},
}
@article{1518,
abstract = {The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno.},
author = {Lohse, Konrad and Chmelik, Martin and Martin, Simon and Barton, Nicholas H},
journal = {Genetics},
number = {2},
pages = {775 -- 786},
publisher = {Genetics Society of America},
title = {{Efficient strategies for calculating blockwise likelihoods under the coalescent}},
doi = {10.1534/genetics.115.183814},
volume = {202},
year = {2016},
}
@article{1522,
abstract = {We classify smooth Brunnian (i.e., unknotted on both components) embeddings (S2 × S1) ⊔ S3 → ℝ6. Any Brunnian embedding (S2 × S1) ⊔ S3 → ℝ6 is isotopic to an explicitly constructed embedding fk,m,n for some integers k, m, n such that m ≡ n (mod 2). Two embeddings fk,m,n and fk′ ,m′,n′ are isotopic if and only if k = k′, m ≡ m′ (mod 2k) and n ≡ n′ (mod 2k). We use Haefliger’s classification of embeddings S3 ⊔ S3 → ℝ6 in our proof. The relation between the embeddings (S2 × S1) ⊔ S3 → ℝ6 and S3 ⊔ S3 → ℝ6 is not trivial, however. For example, we show that there exist embeddings f: (S2 ×S1) ⊔ S3 → ℝ6 and g, g′ : S3 ⊔ S3 → ℝ6 such that the componentwise embedded connected sum f # g is isotopic to f # g′ but g is not isotopic to g′.},
author = {Avvakumov, Serhii},
journal = {Moscow Mathematical Journal},
number = {1},
pages = {1 -- 25},
publisher = {Independent University of Moscow},
title = {{The classification of certain linked 3-manifolds in 6-space}},
volume = {16},
year = {2016},
}
@article{1523,
abstract = {For random graphs, the containment problem considers the probability that a binomial random graph G(n, p) contains a given graph as a substructure. When asking for the graph as a topological minor, i.e., for a copy of a subdivision of the given graph, it is well known that the (sharp) threshold is at p = 1/n. We consider a natural analogue of this question for higher-dimensional random complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k = 2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold for containing a subdivision of any fixed complete 2-complex. For higher dimensions k > 2, we get that p = O(n−1/k) is an upper bound for the threshold probability of containing a subdivision of a fixed k-dimensional complex.},
author = {Gundert, Anna and Wagner, Uli},
journal = {Proceedings of the American Mathematical Society},
number = {4},
pages = {1815 -- 1828},
publisher = {American Mathematical Society},
title = {{On topological minors in random simplicial complexes}},
doi = {10.1090/proc/12824},
volume = {144},
year = {2016},
}
@inproceedings{1524,
abstract = {When designing genetic circuits, the typical primitives used in major existing modelling formalisms are gene interaction graphs, where edges between genes denote either an activation or inhibition relation. However, when designing experiments, it is important to be precise about the low-level mechanistic details as to how each such relation is implemented. The rule-based modelling language Kappa allows to unambiguously specify mechanistic details such as DNA binding sites, dimerisation of transcription factors, or co-operative interactions. Such a detailed description comes with complexity and computationally costly executions. We propose a general method for automatically transforming a rule-based program, by eliminating intermediate species and adjusting the rate constants accordingly. To the best of our knowledge, we show the first automated reduction of rule-based models based on equilibrium approximations.
Our algorithm is an adaptation of an existing algorithm, which was designed for reducing reaction-based programs; our version of the algorithm scans the rule-based Kappa model in search for those interaction patterns known to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional checks are then performed in order to verify if the reduction is meaningful in the context of the full model. The reduced model is efficiently obtained by static inspection over the rule-set. The tool is tested on a detailed rule-based model of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has 11 rules and 5 agents, and provides a dramatic reduction in simulation time of several orders of magnitude.},
author = {Beica, Andreea and Guet, Calin C and Petrov, Tatjana},
location = {Madrid, Spain},
pages = {173 -- 191},
publisher = {Springer},
title = {{Efficient reduction of kappa models by static inspection of the rule-set}},
doi = {10.1007/978-3-319-26916-0_10},
volume = {9271},
year = {2016},
}