@article{822,
  abstract     = {Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. },
  author       = {De Vos, Marjon and Zagórski, Marcin P and Mcnally, Alan and Bollenbach, Mark Tobias},
  issn         = {00278424},
  journal      = {PNAS},
  number       = {40},
  pages        = {10666 -- 10671},
  publisher    = {National Academy of Sciences},
  title        = {{Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections}},
  doi          = {10.1073/pnas.1713372114},
  volume       = {114},
  year         = {2017},
}

@article{823,
  abstract     = {The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region.},
  author       = {Colabrese, Simona and De Martino, Daniele and Leuzzi, Luca and Marinari, Enzo},
  issn         = {17425468},
  journal      = { Journal of Statistical Mechanics: Theory and Experiment},
  number       = {9},
  publisher    = {IOPscience},
  title        = {{Phase transitions in integer linear problems}},
  doi          = {10.1088/1742-5468/aa85c3},
  volume       = {2017},
  year         = {2017},
}

@article{824,
  abstract     = {In shear flows at transitional Reynolds numbers, localized patches of turbulence, known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev. Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds number. Combining slicing methods for continuous symmetry reduction with Poincaré sections for the first time in a shear flow setting, we compute and visualize the unstable manifold of the lower-branch solution and show that it extends towards the neighbourhood of the upper-branch solution. Surprisingly, this connection even persists far above the bifurcation point and appears to mediate the first stage of the puff generation: amplification of streamwise localized fluctuations. When the state-space trajectories on the unstable manifold reach the vicinity of the upper branch, corresponding fluctuations expand in space and eventually take the usual shape of a puff.},
  author       = {Budanur, Nazmi B and Hof, Björn},
  issn         = {00221120},
  journal      = {Journal of Fluid Mechanics},
  publisher    = {Cambridge University Press},
  title        = {{Heteroclinic path to spatially localized chaos in pipe flow}},
  doi          = {10.1017/jfm.2017.516},
  volume       = {827},
  year         = {2017},
}

@article{825,
  abstract     = {What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.},
  author       = {Petritsch, Barbara},
  issn         = {10222588},
  journal      = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare},
  number       = {2},
  pages        = {200 -- 207},
  publisher    = {VÖB},
  title        = {{Metadata for research data in practice}},
  doi          = {10.31263/voebm.v70i2.1678},
  volume       = {70},
  year         = {2017},
}

@inproceedings{833,
  abstract     = {We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams.},
  author       = {Heiss, Teresa and Wagner, Hubert},
  editor       = {Felsberg, Michael and Heyden, Anders and Krüger, Norbert},
  issn         = {03029743},
  location     = {Ystad, Sweden},
  pages        = {397 -- 409},
  publisher    = {Springer},
  title        = {{Streaming algorithm for Euler characteristic curves of multidimensional images}},
  doi          = {10.1007/978-3-319-64689-3_32},
  volume       = {10424},
  year         = {2017},
}

@article{834,
  abstract     = {Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition.},
  author       = {Serbyn, Maksym and Zlatko, Papic and Abanin, Dmitry},
  issn         = {24699950},
  journal      = {Physical Review B - Condensed Matter and Materials Physics},
  number       = {10},
  publisher    = {American Physical Society},
  title        = {{Thouless energy and multifractality across the many-body localization transition}},
  doi          = {10.1103/PhysRevB.96.104201},
  volume       = {96},
  year         = {2017},
}

@inproceedings{836,
  abstract     = {Recent research has examined how to study the topological features of a continuous self-map by means of the persistence of the eigenspaces, for given eigenvalues, of the endomorphism induced in homology over a field. This raised the question of how to select dynamically significant eigenvalues. The present paper aims to answer this question, giving an algorithm that computes the persistence of eigenspaces for every eigenvalue simultaneously, also expressing said eigenspaces as direct sums of “finite” and “singular” subspaces.},
  author       = {Ethier, Marc and Jablonski, Grzegorz and Mrozek, Marian},
  booktitle    = {Special Sessions in Applications of Computer Algebra},
  isbn         = {978-331956930-7},
  location     = {Kalamata, Greece},
  pages        = {119 -- 136},
  publisher    = {Springer},
  title        = {{Finding eigenvalues of self-maps with the Kronecker canonical form}},
  doi          = {10.1007/978-3-319-56932-1_8},
  volume       = {198},
  year         = {2017},
}

@phdthesis{837,
  abstract     = {The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. },
  author       = {Xu, Haibing},
  issn         = {2663-337X},
  pages        = {93},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Reactivation of the hippocampal cognitive map in goal-directed spatial tasks}},
  doi          = {10.15479/AT:ISTA:th_858},
  year         = {2017},
}

@phdthesis{838,
  abstract     = {In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . 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). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. 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, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: 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 + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. },
  author       = {Rybar, Michal},
  issn         = {2663-337X},
  pages        = {86},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{(The exact security of) Message authentication codes}},
  doi          = {10.15479/AT:ISTA:th_828},
  year         = {2017},
}

@phdthesis{839,
  abstract     = {This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material's toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. },
  author       = {Hahn, David},
  issn         = {2663-337X},
  pages        = {124},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Brittle fracture simulation with boundary elements for computer graphics}},
  doi          = {10.15479/AT:ISTA:th_855},
  year         = {2017},
}

@inbook{84,
  abstract     = {The advent of high-throughput technologies and the concurrent advances in information sciences have led to a data revolution in biology. This revolution is most significant in molecular biology, with an increase in the number and scale of the “omics” projects over the last decade. Genomics projects, for example, have produced impressive advances in our knowledge of the information concealed into genomes, from the many genes that encode for the proteins that are responsible for most if not all cellular functions, to the noncoding regions that are now known to provide regulatory functions. Proteomics initiatives help to decipher the role of post-translation modifications on the protein structures and provide maps of protein-protein interactions, while functional genomics is the field that attempts to make use of the data produced by these projects to understand protein functions. The biggest challenge today is to assimilate the wealth of information provided by these initiatives into a conceptual framework that will help us decipher life. For example, the current views of the relationship between protein structure and function remain fragmented. We know of their sequences, more and more about their structures, we have information on their biological activities, but we have difficulties connecting this dotted line into an informed whole. We lack the experimental and computational tools for directly studying protein structure, function, and dynamics at the molecular and supra-molecular levels. In this chapter, we review some of the current developments in building the computational tools that are needed, focusing on the role that geometry and topology play in these efforts. One of our goals is to raise the general awareness about the importance of geometric methods in elucidating the mysterious foundations of our very existence. Another goal is the broadening of what we consider a geometric algorithm. There is plenty of valuable no-man’s-land between combinatorial and numerical algorithms, and it seems opportune to explore this land with a computational-geometric frame of mind.},
  author       = {Edelsbrunner, Herbert and Koehl, Patrice},
  booktitle    = {Handbook of Discrete and Computational Geometry, Third Edition},
  editor       = {Toth, Csaba and O'Rourke, Joseph and Goodman, Jacob},
  pages        = {1709 -- 1735},
  publisher    = {Taylor & Francis},
  title        = {{Computational topology for structural molecular biology}},
  doi          = {10.1201/9781315119601},
  year         = {2017},
}

@article{840,
  abstract     = {Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.},
  author       = {Vukusic, Lada and Kukucka, Josip and Watzinger, Hannes and Katsaros, Georgios},
  issn         = {15306984},
  journal      = {Nano Letters},
  number       = {9},
  pages        = {5706 -- 5710},
  publisher    = {American Chemical Society},
  title        = {{Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry}},
  doi          = {10.1021/acs.nanolett.7b02627},
  volume       = {17},
  year         = {2017},
}

@article{2016,
  abstract     = {The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane.},
  author       = {Martin Del Campo Sanchez, Abraham and Cepeda Humerez, Sarah A and Uhler, Caroline},
  issn         = {03036898},
  journal      = {Scandinavian Journal of Statistics},
  number       = {2},
  pages        = {285 -- 306},
  publisher    = {Wiley-Blackwell},
  title        = {{Exact goodness-of-fit testing for the Ising model}},
  doi          = {10.1111/sjos.12251},
  volume       = {44},
  year         = {2017},
}

@phdthesis{202,
  abstract     = {Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions.},
  author       = {Pleska, Maros},
  issn         = {2663-337X},
  pages        = {126},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Biology of restriction-modification systems at the single-cell and population level}},
  doi          = {10.15479/AT:ISTA:th_916},
  year         = {2017},
}

@article{662,
  abstract     = {We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays.},
  author       = {Shi, Liang and Hof, Björn and Rampp, Markus and Avila, Marc},
  issn         = {10706631},
  journal      = {Physics of Fluids},
  number       = {4},
  publisher    = {American Institute of Physics},
  title        = {{Hydrodynamic turbulence in quasi Keplerian rotating flows}},
  doi          = {10.1063/1.4981525},
  volume       = {29},
  year         = {2017},
}

@inproceedings{663,
  abstract     = {In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. },
  author       = {Kong, Hui and Bogomolov, Sergiy and Schilling, Christian and Jiang, Yu and Henzinger, Thomas A},
  booktitle    = {Proceedings of the 20th International Conference on Hybrid Systems},
  isbn         = {978-145034590-3},
  location     = {Pittsburgh, PA, United States},
  pages        = {163 -- 172},
  publisher    = {ACM},
  title        = {{Safety verification of nonlinear hybrid systems based on invariant clusters}},
  doi          = {10.1145/3049797.3049814},
  year         = {2017},
}

@article{664,
  abstract     = {Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it.},
  author       = {Assen, Frank P and Sixt, Michael K},
  issn         = {10747613},
  journal      = {Immunity},
  number       = {4},
  pages        = {519 -- 520},
  publisher    = {Cell Press},
  title        = {{The dynamic cytokine niche}},
  doi          = {10.1016/j.immuni.2017.04.006},
  volume       = {46},
  year         = {2017},
}

@article{665,
  abstract     = {The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria.},
  author       = {Bergmiller, Tobias and Andersson, Anna M and Tomasek, Kathrin and Balleza, Enrique and Kiviet, Daniel and Hauschild, Robert and Tkacik, Gasper and Guet, Calin C},
  issn         = {00368075},
  journal      = {Science},
  number       = {6335},
  pages        = {311 -- 315},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity}},
  doi          = {10.1126/science.aaf4762},
  volume       = {356},
  year         = {2017},
}

@article{666,
  abstract     = {Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors.},
  author       = {Mitosch, Karin and Rieckh, Georg and Bollenbach, Tobias},
  issn         = {24054712},
  journal      = {Cell Systems},
  number       = {4},
  pages        = {393 -- 403},
  publisher    = {Cell Press},
  title        = {{Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment}},
  doi          = {10.1016/j.cels.2017.03.001},
  volume       = {4},
  year         = {2017},
}

@article{667,
  abstract     = {Perinatal exposure to penicillin may result in longlasting gut and behavioral changes.},
  author       = {Novarino, Gaia},
  issn         = {19466234},
  journal      = {Science Translational Medicine},
  number       = {387},
  publisher    = {American Association for the Advancement of Science},
  title        = {{The antisocial side of antibiotics}},
  doi          = {10.1126/scitranslmed.aan2786},
  volume       = {9},
  year         = {2017},
}