@article{1434,
  abstract     = {We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B   are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B   on scales down to N−2/3N−2/3.},
  author       = {Bao, Zhigang and Erdös, László and Schnelli, Kevin},
  journal      = {Journal of Functional Analysis},
  number       = {3},
  pages        = {672 -- 719},
  publisher    = {Academic Press},
  title        = {{Local stability of the free additive convolution}},
  doi          = {10.1016/j.jfa.2016.04.006},
  volume       = {271},
  year         = {2016},
}

@article{1435,
  abstract     = {ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states.},
  author       = {Guzmán, José and Gerevich, Zoltan},
  journal      = {Neural Plasticity},
  publisher    = {Hindawi Publishing Corporation},
  title        = {{P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction}},
  doi          = {10.1155/2016/1207393},
  volume       = {2016},
  year         = {2016},
}

@article{1436,
  abstract     = {We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system.},
  author       = {Bach, Volker and Breteaux, Sébastien and Petrat, Sören P and Pickl, Peter and Tzaneteas, Tim},
  journal      = {Journal de Mathématiques Pures et Appliquées},
  number       = {1},
  pages        = {1 -- 30},
  publisher    = {Elsevier},
  title        = {{Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction}},
  doi          = {10.1016/j.matpur.2015.09.003},
  volume       = {105},
  year         = {2016},
}

@inproceedings{1438,
  abstract     = {In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism.},
  author       = {Chatterjee, Krishnendu and Fu, Hongfei and Novotny, Petr and Hasheminezhad, Rouzbeh},
  location     = {St. Petersburg, FL, USA},
  pages        = {327 -- 342},
  publisher    = {ACM},
  title        = {{Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs}},
  doi          = {10.1145/2837614.2837639},
  volume       = {20-22},
  year         = {2016},
}

@inproceedings{1439,
  abstract     = {Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification.},
  author       = {Dragoi, Cezara and Henzinger, Thomas A and Zufferey, Damien},
  location     = {St. Petersburg, FL, USA},
  pages        = {400 -- 415},
  publisher    = {ACM},
  title        = {{PSYNC: A partially synchronous language for fault-tolerant distributed algorithms}},
  doi          = {10.1145/2837614.2837650},
  volume       = {20-22},
  year         = {2016},
}

@article{1440,
  author       = {Janovjak, Harald L},
  journal      = {Structure},
  number       = {2},
  pages        = {213 -- 215},
  publisher    = {Cell Press},
  title        = {{Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain}},
  doi          = {10.1016/j.str.2016.01.002},
  volume       = {24},
  year         = {2016},
}

@article{1446,
  abstract     = {The accuracy of interdisciplinarity measurements is directly related to the quality of the underlying bibliographic data. Existing indicators of interdisciplinarity are not capable of reflecting the inaccuracies introduced by incorrect and incomplete records because correct and complete bibliographic data can rarely be obtained. This is the case for the Rao–Stirling index, which cannot handle references that are not categorized into disciplinary fields. We introduce a method that addresses this problem. It extends the Rao–Stirling index to acknowledge missing data by calculating its interval of uncertainty using computational optimization. The evaluation of our method indicates that the uncertainty interval is not only useful for estimating the inaccuracy of interdisciplinarity measurements, but it also delivers slightly more accurate aggregated interdisciplinarity measurements than the Rao–Stirling index.},
  author       = {Calatrava Moreno, Maria and Auzinger, Thomas and Werthner, Hannes},
  journal      = {Scientometrics},
  number       = {1},
  pages        = {213 -- 232},
  publisher    = {Springer},
  title        = {{On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data}},
  doi          = {10.1007/s11192-016-1842-4},
  volume       = {107},
  year         = {2016},
}

@article{1448,
  abstract     = {We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli–Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities.},
  author       = {Fathi, Max and Maas, Jan},
  journal      = {The Annals of Applied Probability},
  number       = {3},
  pages        = {1774 -- 1806},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Entropic Ricci curvature bounds for discrete interacting systems}},
  doi          = {10.1214/15-AAP1133},
  volume       = {26},
  year         = {2016},
}

@article{1794,
  abstract     = {We consider Conditional random fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) (Formula presented.) is the sum of terms over intervals [i, j] where each term is non-zero only if the substring (Formula presented.) equals a prespecified pattern w. Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.) where L is the combined length of input patterns, (Formula presented.) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.), where (Formula presented.) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights.},
  author       = {Kolmogorov, Vladimir and Takhanov, Rustem},
  journal      = {Algorithmica},
  number       = {1},
  pages        = {17 -- 46},
  publisher    = {Springer},
  title        = {{Inference algorithms for pattern-based CRFs on sequence data}},
  doi          = {10.1007/s00453-015-0017-7},
  volume       = {76},
  year         = {2016},
}

@article{1833,
  abstract     = {Relational models for contingency tables are generalizations of log-linear models, allowing effects associated with arbitrary subsets of cells in the table, and not necessarily containing the overall effect, that is, a common parameter in every cell. Similarly to log-linear models, relational models can be extended to non-negative distributions, but the extension requires more complex methods. An extended relational model is defined as an algebraic variety, and it turns out to be the closure of the original model with respect to the Bregman divergence. In the extended relational model, the MLE of the cell parameters always exists and is unique, but some of its properties may be different from those of the MLE under log-linear models. The MLE can be computed using a generalized iterative scaling procedure based on Bregman projections. },
  author       = {Klimova, Anna and Rudas, Tamás},
  journal      = {Journal of Multivariate Analysis},
  pages        = {440 -- 452},
  publisher    = {Elsevier},
  title        = {{On the closure of relational models}},
  doi          = {10.1016/j.jmva.2015.10.005},
  volume       = {143},
  year         = {2016},
}

@inproceedings{1227,
  abstract     = {Many biological systems can be modeled as multiaffine hybrid systems. Due to the nonlinearity of multiaffine systems, it is difficult to verify their properties of interest directly. A common strategy to tackle this problem is to construct and analyze a discrete overapproximation of the original system. However, the conservativeness of a discrete abstraction significantly determines the level of confidence we can have in the properties of the original system. In this paper, in order to reduce the conservativeness of a discrete abstraction, we propose a new method based on a sufficient and necessary decision condition for computing discrete transitions between states in the abstract system. We assume the state space partition of a multiaffine system to be based on a set of multivariate polynomials. Hence, a rectangular partition defined in terms of polynomials of the form (xi − c) is just a simple case of multivariate polynomial partition, and the new decision condition applies naturally. We analyze and demonstrate the improvement of our method over the existing methods using some examples.},
  author       = {Kong, Hui and Bartocci, Ezio and Bogomolov, Sergiy and Grosu, Radu and Henzinger, Thomas A and Jiang, Yu and Schilling, Christian},
  location     = {Grenoble, France},
  pages        = {128 -- 144},
  publisher    = {Springer},
  title        = {{Discrete abstraction of multiaffine systems}},
  doi          = {10.1007/978-3-319-47151-8_9},
  volume       = {9957},
  year         = {2016},
}

@inproceedings{1231,
  abstract     = {We study the time-and memory-complexities of the problem of computing labels of (multiple) randomly selected challenge-nodes in a directed acyclic graph. The w-bit label of a node is the hash of the labels of its parents, and the hash function is modeled as a random oracle. Specific instances of this problem underlie both proofs of space [Dziembowski et al. CRYPTO’15] as well as popular memory-hard functions like scrypt. As our main tool, we introduce the new notion of a probabilistic parallel entangled pebbling game, a new type of combinatorial pebbling game on a graph, which is closely related to the labeling game on the same graph. As a first application of our framework, we prove that for scrypt, when the underlying hash function is invoked n times, the cumulative memory complexity (CMC) (a notion recently introduced by Alwen and Serbinenko (STOC’15) to capture amortized memory-hardness for parallel adversaries) is at least Ω(w · (n/ log(n))2). This bound holds for adversaries that can store many natural functions of the labels (e.g., linear combinations), but still not arbitrary functions thereof. We then introduce and study a combinatorial quantity, and show how a sufficiently small upper bound on it (which we conjecture) extends our CMC bound for scrypt to hold against arbitrary adversaries. We also show that such an upper bound solves the main open problem for proofs-of-space protocols: namely, establishing that the time complexity of computing the label of a random node in a graph on n nodes (given an initial kw-bit state) reduces tightly to the time complexity for black pebbling on the same graph (given an initial k-node pebbling).},
  author       = {Alwen, Joel F and Chen, Binyi and Kamath Hosdurg, Chethan and Kolmogorov, Vladimir and Pietrzak, Krzysztof Z and Tessaro, Stefano},
  location     = {Vienna, Austria},
  pages        = {358 -- 387},
  publisher    = {Springer},
  title        = {{On the complexity of scrypt and proofs of space in the parallel random oracle model}},
  doi          = {10.1007/978-3-662-49896-5_13},
  volume       = {9666},
  year         = {2016},
}

@article{1232,
  abstract     = {Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIII 2 CIV (the respirasome) - a major 'tight' form and a minor 'loose' form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII 2 at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.},
  author       = {Letts, James A and Fiedorczuk, Karol and Sazanov, Leonid A},
  journal      = {Nature},
  number       = {7622},
  pages        = {644 -- 648},
  publisher    = {Nature Publishing Group},
  title        = {{The architecture of respiratory supercomplexes}},
  doi          = {10.1038/nature19774},
  volume       = {537},
  year         = {2016},
}

@inproceedings{1233,
  abstract     = {About three decades ago it was realized that implementing private channels between parties which can be adaptively corrupted requires an encryption scheme that is secure against selective opening attacks. Whether standard (IND-CPA) security implies security against selective opening attacks has been a major open question since. The only known reduction from selective opening to IND-CPA security loses an exponential factor. A polynomial reduction is only known for the very special case where the distribution considered in the selective opening security experiment is a product distribution, i.e., the messages are sampled independently from each other. In this paper we give a reduction whose loss is quantified via the dependence graph (where message dependencies correspond to edges) of the underlying message distribution. In particular, for some concrete distributions including Markov distributions, our reduction is polynomial.},
  author       = {Fuchsbauer, Georg and Heuer, Felix and Kiltz, Eike and Pietrzak, Krzysztof Z},
  location     = {Tel Aviv, Israel},
  pages        = {282 -- 305},
  publisher    = {Springer},
  title        = {{Standard security does imply security against selective opening for markov distributions}},
  doi          = {10.1007/978-3-662-49096-9_12},
  volume       = {9562},
  year         = {2016},
}

@inproceedings{1237,
  abstract     = {Bitmap images of arbitrary dimension may be formally perceived as unions of m-dimensional boxes aligned with respect to a rectangular grid in ℝm. Cohomology and homology groups are well known topological invariants of such sets. Cohomological operations, such as the cup product, provide higher-order algebraic topological invariants, especially important for digital images of dimension higher than 3. If such an operation is determined at the level of simplicial chains [see e.g. González-Díaz, Real, Homology, Homotopy Appl, 2003, 83-93], then it is effectively computable. However, decomposing a cubical complex into a simplicial one deleteriously affects the efficiency of such an approach. In order to avoid this overhead, a direct cubical approach was applied in [Pilarczyk, Real, Adv. Comput. Math., 2015, 253-275] for the cup product in cohomology, and implemented in the ChainCon software package [http://www.pawelpilarczyk.com/chaincon/]. We establish a formula for the Steenrod square operations [see Steenrod, Annals of Mathematics. Second Series, 1947, 290-320] directly at the level of cubical chains, and we prove the correctness of this formula. An implementation of this formula is programmed in C++ within the ChainCon software framework. We provide a few examples and discuss the effectiveness of this approach. One specific application follows from the fact that Steenrod squares yield tests for the topological extension problem: Can a given map A → Sd to a sphere Sd be extended to a given super-complex X of A? In particular, the ROB-SAT problem, which is to decide for a given function f: X → ℝm and a value r &gt; 0 whether every g: X → ℝm with ∥g - f ∥∞ ≤ r has a root, reduces to the extension problem.},
  author       = {Krcál, Marek and Pilarczyk, Pawel},
  location     = {Marseille, France},
  pages        = {140 -- 151},
  publisher    = {Springer},
  title        = {{Computation of cubical Steenrod squares}},
  doi          = {10.1007/978-3-319-39441-1_13},
  volume       = {9667},
  year         = {2016},
}

@article{1238,
  abstract     = {The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes—termed herein as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth.},
  author       = {Von Wangenheim, Daniel and Rosero, Amparo and Komis, George and Šamajová, Olga and Ovečka, Miroslav and Voigt, Boris and Šamaj, Jozef},
  journal      = {Frontiers in Plant Science},
  number       = {JAN2016},
  publisher    = {Frontiers Research Foundation},
  title        = {{Endosomal interactions during root hair growth}},
  doi          = {10.3389/fpls.2015.01262},
  volume       = {6},
  year         = {2016},
}

@article{1239,
  abstract     = {Nonadherent polarized cells have been observed to have a pearlike, elongated shape. Using a minimal model that describes the cell cortex as a thin layer of contractile active gel, we show that the anisotropy of active stresses, controlled by cortical viscosity and filament ordering, can account for this morphology. The predicted shapes can be determined from the flow pattern only; they prove to be independent of the mechanism at the origin of the cortical flow, and are only weakly sensitive to the cytoplasmic rheology. In the case of actin flows resulting from a contractile instability, we propose a phase diagram of three-dimensional cell shapes that encompasses nonpolarized spherical, elongated, as well as oblate shapes, all of which have been observed in experiment.},
  author       = {Callan Jones, Andrew and Ruprecht, Verena and Wieser, Stefan and Heisenberg, Carl-Philipp J and Voituriez, Raphaël},
  journal      = {Physical Review Letters},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Cortical flow-driven shapes of nonadherent cells}},
  doi          = {10.1103/PhysRevLett.116.028102},
  volume       = {116},
  year         = {2016},
}

@article{1240,
  abstract     = {Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at 1- or more than 1-month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in two independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers.},
  author       = {Kornienko, Aleksandra and Dotter, Christoph and Guenzl, Philipp and Gisslinger, Heinz and Gisslinger, Bettina and Cleary, Ciara and Kralovics, Robert and Pauler, Florian and Barlow, Denise},
  journal      = {Genome Biology},
  number       = {1},
  publisher    = {BioMed Central},
  title        = {{Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans}},
  doi          = {10.1186/s13059-016-0873-8},
  volume       = {17},
  year         = {2016},
}

@article{1241,
  abstract     = {How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances.},
  author       = {Uecker, Hildegard and Hermisson, Joachim},
  journal      = {Genetics},
  number       = {2},
  pages        = {721 -- 732},
  publisher    = {Genetics Society of America},
  title        = {{The role of recombination in evolutionary rescue}},
  doi          = {10.1534/genetics.115.180299},
  volume       = {202},
  year         = {2016},
}

@article{1242,
  abstract     = {A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression.},
  author       = {Sokolowski, Thomas R and Walczak, Aleksandra and Bialek, William and Tkacik, Gasper},
  journal      = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
  number       = {2},
  publisher    = {American Institute of Physics},
  title        = {{Extending the dynamic range of transcription factor action by translational regulation}},
  doi          = {10.1103/PhysRevE.93.022404},
  volume       = {93},
  year         = {2016},
}

