@inproceedings{1179,
abstract = {Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another.
Such chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.)
A variable X has k bits of HILL entropy of quality (ϵ,s)
if there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ
by distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists.
We first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s)
, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2)
in circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality).
The chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s)
, then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound.},
author = {Pietrzak, Krzysztof Z and Maciej, Skorski},
location = {Beijing, China},
pages = {183 -- 203},
publisher = {Springer},
title = {{Pseudoentropy: Lower-bounds for chain rules and transformations}},
doi = {10.1007/978-3-662-53641-4_8},
volume = {9985},
year = {2016},
}
@article{1181,
abstract = {This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies.},
author = {Dwyer, Noelle and Chen, Bin and Chou, Shen and Hippenmeyer, Simon and Nguyen, Laurent and Ghashghaei, Troy},
journal = {Journal of Neuroscience},
number = {45},
pages = {11394 -- 11401},
publisher = {Society for Neuroscience},
title = {{Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity}},
doi = {10.1523/JNEUROSCI.2359-16.2016},
volume = {36},
year = {2016},
}
@inproceedings{1182,
abstract = {Balanced knockout tournaments are ubiquitous in sports competitions and are also used in decisionmaking and elections. The traditional computational question, that asks to compute a draw (optimal draw) that maximizes the winning probability for a distinguished player, has received a lot of attention. Previous works consider the problem where the pairwise winning probabilities are known precisely, while we study how robust is the winning probability with respect to small errors in the pairwise winning probabilities. First, we present several illuminating examples to establish: (a) there exist deterministic tournaments (where the pairwise winning probabilities are 0 or 1) where one optimal draw is much more robust than the other; and (b) in general, there exist tournaments with slightly suboptimal draws that are more robust than all the optimal draws. The above examples motivate the study of the computational problem of robust draws that guarantee a specified winning probability. Second, we present a polynomial-time algorithm for approximating the robustness of a draw for sufficiently small errors in pairwise winning probabilities, and obtain that the stated computational problem is NP-complete. We also show that two natural cases of deterministic tournaments where the optimal draw could be computed in polynomial time also admit polynomial-time algorithms to compute robust optimal draws.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Tkadlec, Josef},
location = {New York, NY, USA},
pages = {172 -- 179},
publisher = {AAAI Press},
title = {{Robust draws in balanced knockout tournaments}},
volume = {2016-January},
year = {2016},
}
@article{1184,
abstract = {Across multicellular organisms, the costs of reproduction and self-maintenance result in a life history trade-off between fecundity and longevity. Queens of perennial social Hymenoptera are both highly fertile and long-lived, and thus, this fundamental trade-off is lacking. Whether social insect males similarly evade the fecundity/longevity trade-off remains largely unstudied. Wingless males of the ant genus Cardiocondyla stay in their natal colonies throughout their relatively long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla obscurior males that were allowed to mate with large numbers of female sexuals had a shortened life span compared to males that mated at a low frequency or virgin males. Although frequent mating negatively affects longevity, males clearly benefit from a “live fast, die young strategy” by inseminating as many female sexuals as possible at a cost to their own survival.},
author = {Metzler, Sina and Heinze, Jürgen and Schrempf, Alexandra},
journal = {Ecology and Evolution},
number = {24},
pages = {8903 -- 8906},
publisher = {Wiley-Blackwell},
title = {{Mating and longevity in ant males}},
doi = {10.1002/ece3.2474},
volume = {6},
year = {2016},
}
@article{1185,
abstract = {The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk.},
author = {Cucinotta, Mara and Manrique, Silvia and Guazzotti, Andrea and Quadrelli, Nadia and Mendes, Marta and Benková, Eva and Colombo, Lucia},
journal = {Development},
number = {23},
pages = {4419 -- 4424},
publisher = {Company of Biologists},
title = {{Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development}},
doi = {10.1242/dev.143545},
volume = {143},
year = {2016},
}
@article{1186,
abstract = {The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.},
author = {Gutierrez-Fernandez, Javier and Saleh, Malek and Alcorlo, Martín and Gómez Mejóa, Alejandro and Pantoja Uceda, David and Treviño, Miguel and Vob, Franziska and Abdullah, Mohammed and Galán Bartual, Sergio and Seinen, Jolien and Sánchez Murcia, Pedro and Gago, Federico and Bruix, Marta and Hammerschmidt, Sven and Hermoso, Juan},
journal = {Scientific Reports},
publisher = {Nature Publishing Group},
title = {{Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis}},
doi = {10.1038/srep38094},
volume = {6},
year = {2016},
}
@article{1188,
abstract = {We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling.
In the asymptotic regime of slow
diffusion, that coincides with the relevant experimental range, the resulting
non-linear Fokker–Planck equation is solved for the steady state in the WKB
approximation that maps it into the ground state of a quantum particle in an
Airy potential plus a centrifugal term. We retrieve scaling laws for growth rate
fluctuations and time response with respect to the distance from the maximum
growth rate suggesting that suboptimal populations can have a faster response
to perturbations.},
author = {De Martino, Daniele and Masoero, Davide},
journal = { Journal of Statistical Mechanics: Theory and Experiment},
number = {12},
publisher = {IOPscience},
title = {{Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth}},
doi = {10.1088/1742-5468/aa4e8f},
volume = {2016},
year = {2016},
}
@phdthesis{1189,
abstract = {Within the scope of this thesis, we show that a driven-dissipative system with
few ultracold atoms can exhibit dissipatively bound states, even if the atom-atom
interaction is purely repulsive. This bond arises due to the dipole-dipole inter-
action, which is restricted to one of the lower electronic energy states, resulting
in the distance-dependent coherent population trapping. The quality of this al-
ready established method of dissipative binding is improved and the application
is extended to higher dimensions and a larger number of atoms. Here, we simu-
late two- and three-atom systems using an adapted approach to the Monte Carlo
wave-function method and analyse the results. Finally, we examine the possi-
bility of finding a setting allowing trimer states but prohibiting dimer states.
In the context of open quantum systems, such a three-body bound states corre-
sponds to the driven-dissipative analogue of a Borromean state. These states can
be detected in modern experiments with dipolar and Rydberg-dressed ultracold
atomic gases.
},
author = {Jochum, Clemens},
pages = {94},
publisher = {Technical University Vienna},
title = {{Dissipative Few-Body Quantum Systems}},
year = {2016},
}
@inproceedings{1193,
abstract = {We consider the recent formulation of the Algorithmic Lovász Local Lemma [1], [2] for finding objects that avoid "bad features", or "flaws". It extends the Moser-Tardos resampling algorithm [3] to more general discrete spaces. At each step the method picks a flaw present in the current state and "resamples" it using a "resampling oracle" provided by the user. However, it is less flexible than the Moser-Tardos method since [1], [2] require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and thus can potentially be implemented more efficiently). We formulate a new "commutativity" condition, and prove that it is sufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additional assumption. We then show that existing resampling oracles for perfect matchings and permutations do satisfy this condition. Finally, we generalize the precondition in [2] (in the case of symmetric potential causality graphs). This unifies special cases that previously were treated separately.},
author = {Kolmogorov, Vladimir},
booktitle = {Proceedings - Annual IEEE Symposium on Foundations of Computer Science},
location = {New Brunswick, NJ, USA },
publisher = {IEEE},
title = {{Commutativity in the algorithmic Lovasz local lemma}},
doi = {10.1109/FOCS.2016.88},
volume = {2016-December},
year = {2016},
}
@article{1195,
abstract = {The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. },
author = {Franssen, Susan and Barton, Nicholas H and Schlötterer, Christian},
journal = {Molecular Biology and Evolution},
number = {1},
pages = {174 -- 184},
publisher = {Oxford University Press},
title = {{Reconstruction of haplotype-blocks selected during experimental evolution.}},
doi = {10.1093/molbev/msw210},
volume = {34},
year = {2016},
}
@article{1197,
abstract = {Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.},
author = {Prentice, Jason and Marre, Olivier and Ioffe, Mark and Loback, Adrianna and Tkacik, Gasper and Berry, Michael},
journal = {PLoS Computational Biology},
number = {11},
publisher = {Public Library of Science},
title = {{Error-robust modes of the retinal population code}},
doi = {10.1371/journal.pcbi.1005148},
volume = {12},
year = {2016},
}
@article{1200,
author = {Hilbe, Christian and Traulsen, Arne},
journal = {Physics of Life Reviews},
pages = {29 -- 31},
publisher = {Elsevier},
title = {{Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze}},
doi = {10.1016/j.plrev.2016.10.004},
volume = {19},
year = {2016},
}
@article{1201,
abstract = {In this issue of Cell, Skau et al. show that the formin FMN2 organizes a perinuclear actin cytoskeleton that protects the nucleus and its genomic content of migrating cells squeezing through small spaces.},
author = {Renkawitz, Jörg and Sixt, Michael K},
journal = {Cell},
number = {6},
pages = {1448 -- 1449},
publisher = {Cell Press},
title = {{Formin’ a nuclear protection}},
doi = {10.1016/j.cell.2016.11.024},
volume = {167},
year = {2016},
}
@article{1202,
author = {Milutinovic, Barbara and Peuß, Robert and Ferro, Kevin and Kurtz, Joachim},
journal = {Zoology },
number = {4},
pages = {254 -- 261},
publisher = {Elsevier},
title = {{Immune priming in arthropods: an update focusing on the red flour beetle}},
doi = {10.1016/j.zool.2016.03.006},
volume = {119},
year = {2016},
}
@article{1203,
abstract = {Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae.},
author = {Hu, Fang and Rishishwar, Lavanya and Sivadas, Ambily and Mitchell, Gabriel and King, Jordan and Murphy, Timothy and Gilsdorf, Janet and Mayer, Leonard and Wang, Xin},
journal = {Journal of Clinical Microbiology},
number = {12},
pages = {3010 -- 3017},
publisher = {American Society for Microbiology},
title = {{Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination}},
doi = {10.1128/JCM.01511-16},
volume = {54},
year = {2016},
}
@article{1204,
abstract = {In science, as in life, "surprises" can be adequately appreciated only in the presence of a null model, what we expect a priori. In physics, theories sometimes express the values of dimensionless physical constants as combinations of mathematical constants like π or e. The inverse problem also arises, whereby the measured value of a physical constant admits a "surprisingly" simple approximation in terms of well-known mathematical constants. Can we estimate the probability for this to be a mere coincidence, rather than an inkling of some theory? We answer the question in the most naive form.},
author = {Amir, Ariel and Lemeshko, Mikhail and Tokieda, Tadashi},
journal = {American Mathematical Monthly},
number = {6},
pages = {609 -- 612},
publisher = {Mathematical Association of America},
title = {{Surprises in numerical expressions of physical constants}},
doi = {10.4169/amer.math.monthly.123.6.609},
volume = {123},
year = {2016},
}
@inproceedings{1205,
abstract = {In this paper, we present a formal model-driven engineering approach to establishing a safety-assured implementation of Multifunction vehicle bus controller (MVBC) based on the generic reference models and requirements described in the International Electrotechnical Commission (IEC) standard IEC-61375. First, the generic models described in IEC-61375 are translated into a network of timed automata, and some safety requirements tested in IEC-61375 are formalized as timed computation tree logic (TCTL) formulas. With the help of Uppaal, we check and debug whether the timed automata satisfy the formulas or not. Within this step, several logic inconsistencies in the original standard are detected and corrected. Then, we apply the tool Times to generate C code from the verified model, which was later synthesized into a real MVBC chip. Finally, the runtime verification tool RMOR is applied to verify some safety requirements at the implementation level. We set up a real platform with worldwide mostly used MVBC D113, and verify the correctness and the scalability of the synthesized MVBC chip more comprehensively. The errors in the standard has been confirmed and the resulted MVBC has been deployed in real train communication network.},
author = {Jiang, Yu and Liu, Han and Song, Houbing and Kong, Hui and Gu, Ming and Sun, Jiaguang and Sha, Lui},
location = {Limassol, Cyprus},
pages = {757 -- 763},
publisher = {Springer},
title = {{Safety assured formal model driven design of the multifunction vehicle bus controller}},
doi = {10.1007/978-3-319-48989-6_47},
volume = {9995},
year = {2016},
}
@article{1206,
abstract = {We study a polar molecule immersed in a superfluid environment, such as a helium nanodroplet or a Bose–Einstein condensate, in the presence of a strong electrostatic field. We show that coupling of the molecular pendular motion, induced by the field, to the fluctuating bath leads to formation of pendulons—spherical harmonic librators dressed by a field of many-particle excitations. We study the behavior of the pendulon in a broad range of molecule–bath and molecule–field interaction strengths, and reveal that its spectrum features a series of instabilities which are absent in the field-free case of the angulon quasiparticle. Furthermore, we show that an external field allows to fine-tune the positions of these instabilities in the molecular rotational spectrum. This opens the door to detailed experimental studies of redistribution of orbital angular momentum in many-particle systems. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim},
author = {Redchenko, Elena and Lemeshko, Mikhail},
journal = {ChemPhysChem},
number = {22},
pages = {3649 -- 3654},
publisher = {Wiley-Blackwell},
title = {{Libration of strongly oriented polar molecules inside a superfluid}},
doi = {10.1002/cphc.201601042},
volume = {17},
year = {2016},
}
@article{1209,
abstract = {NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the least characterized complex of the mitochondrial electron transport chain. Because of the ease of sample availability, previous work has focused almost exclusively on bovine complex I. However, only medium resolution structural analyses of this complex have been reported. Working with other mammalian complex I homologues is a potential approach for overcoming these limitations. Due to the inherent difficulty of expressing large membrane protein complexes, screening of complex I homologues is limited to large mammals reared for human consumption. The high sequence identity among these available sources may preclude the benefits of screening. Here, we report the characterization of complex I purified from Ovis aries (ovine) heart mitochondria. All 44 unique subunits of the intact complex were identified by mass spectrometry. We identified differences in the subunit composition of subcomplexes of ovine complex I as compared with bovine, suggesting differential stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa subunit, which is easily lost from the bovine enzyme, remains tightly bound to ovine complex I. Additionally, we developed a novel purification protocol for highly active and stable mitochondrial complex I using the branched-chain detergent lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related, significant differences exist between the biochemical properties of complex I prepared from ovine and bovine mitochondria and that ovine complex I represents a suitable alternative target for further structural studies. },
author = {Letts, James A and Degliesposti, Gianluca and Fiedorczuk, Karol and Skehel, Mark and Sazanov, Leonid A},
journal = {Journal of Biological Chemistry},
number = {47},
pages = {24657 -- 24675},
publisher = {American Society for Biochemistry and Molecular Biology},
title = {{Purification of ovine respiratory complex i results in a highly active and stable preparation}},
doi = {10.1074/jbc.M116.735142},
volume = {291},
year = {2016},
}
@inbook{1210,
abstract = {Mechanisms for cell protection are essential for survival of multicellular organisms. In plants, the apical hook, which is transiently formed in darkness when the germinating seedling penetrates towards the soil surface, plays such protective role and shields the vitally important shoot apical meristem and cotyledons from damage. The apical hook is formed by bending of the upper hypocotyl soon after germination, and it is maintained in a closed stage while the hypocotyl continues to penetrate through the soil and rapidly opens when exposed to light in proximity of the soil surface. To uncover the complex molecular network orchestrating this spatiotemporally tightly coordinated process, monitoring of the apical hook development in real time is indispensable. Here we describe an imaging platform that enables high-resolution kinetic analysis of this dynamic developmental process. © Springer Science+Business Media New York 2017.},
author = {Zhu, Qiang and Žádníková, Petra and Smet, Dajo and Van Der Straeten, Dominique and Benková, Eva},
booktitle = {Plant Hormones},
pages = {1 -- 8},
publisher = {Humana Press},
title = {{Real time analysis of the apical hook development}},
doi = {10.1007/978-1-4939-6469-7_1},
volume = {1497},
year = {2016},
}
@article{1212,
abstract = {Plants adjust their growth according to gravity. Gravitropism involves gravity perception, signal transduction, and asymmetric growth response, with organ bending as a consequence [1]. Asymmetric growth results from the asymmetric distribution of the plant-specific signaling molecule auxin [2] that is generated by lateral transport, mediated in the hypocotyl predominantly by the auxin transporter PIN-FORMED3 (PIN3) [3–5]. Gravity stimulation polarizes PIN3 to the bottom sides of endodermal cells, correlating with increased auxin accumulation in adjacent tissues at the lower side of the stimulated organ, where auxin induces cell elongation and, hence, organ bending. A curvature response allows the hypocotyl to resume straight growth at a defined angle [6], implying that at some point auxin symmetry is restored to prevent overbending. Here, we present initial insights into cellular and molecular mechanisms that lead to the termination of the tropic response. We identified an auxin feedback on PIN3 polarization as underlying mechanism that restores symmetry of the PIN3-dependent auxin flow. Thus, two mechanistically distinct PIN3 polarization events redirect auxin fluxes at different time points of the gravity response: first, gravity-mediated redirection of PIN3-mediated auxin flow toward the lower hypocotyl side, where auxin gradually accumulates and promotes growth, and later PIN3 polarization to the opposite cell side, depleting this auxin maximum to end the bending. Accordingly, genetic or pharmacological interference with the late PIN3 polarization prevents termination of the response and leads to hypocotyl overbending. This observation reveals a role of auxin feedback on PIN polarity in the termination of the tropic response. © 2016 Elsevier Ltd},
author = {Rakusová, Hana and Abbas, Mohamad and Han, Huibin and Song, Siyuan and Robert, Hélène and Friml, Jirí},
journal = {Current Biology},
number = {22},
pages = {3026 -- 3032},
publisher = {Cell Press},
title = {{Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity}},
doi = {10.1016/j.cub.2016.08.067},
volume = {26},
year = {2016},
}
@inproceedings{1214,
abstract = {With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. While very successful with classical robots, these methods run into severe difficulties when applied to soft robots, a new field of robotics with large interest for human-robot interaction. We claim that a novel controller paradigm opens new perspective for this field. This paper applies a recently developed neuro controller with differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently develops to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.},
author = {Martius, Georg S and Hostettler, Raphael and Knoll, Alois and Der, Ralf},
location = {Daejeon, Korea},
publisher = {IEEE},
title = {{Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm}},
doi = {10.1109/IROS.2016.7759138},
volume = {2016-November},
year = {2016},
}
@article{1216,
abstract = {A framework fo r extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance is proposed in this paper. The minima of the acceleration magnitude (a superset of acceleration zeros) are extracted and discriminated into vortices and saddle points, based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These feature points are tracked in time with a robust algorithm for tracking features. Thus, a space-time hierarchy of the minima is built and vortex merging events are detected. We apply the acceleration feature extraction strategy to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of the pressure field and minima of λ2.},
author = {Kasten, Jens and Reininghaus, Jan and Hotz, Ingrid and Hege, Hans and Noack, Bernd and Daviller, Guillaume and Morzyński, Marek},
journal = {Archives of Mechanics},
number = {1},
pages = {55 -- 80},
publisher = {Polish Academy of Sciences Publishing House},
title = {{Acceleration feature points of unsteady shear flows}},
volume = {68},
year = {2016},
}
@article{1217,
abstract = {Understanding the regulation of T-cell responses during inflammation and auto-immunity is fundamental for designing efficient therapeutic strategies against immune diseases. In this regard, prostaglandin E 2 (PGE 2) is mostly considered a myeloid-derived immunosuppressive molecule. We describe for the first time that T cells secrete PGE 2 during T-cell receptor stimulation. In addition, we show that autocrine PGE 2 signaling through EP receptors is essential for optimal CD4 + T-cell activation in vitro and in vivo, and for T helper 1 (Th1) and regulatory T cell differentiation. PGE 2 was found to provide additive co-stimulatory signaling through AKT activation. Intravital multiphoton microscopy showed that triggering EP receptors in T cells is also essential for the stability of T cell-dendritic cell (DC) interactions and Th-cell accumulation in draining lymph nodes (LNs) during inflammation. We further demonstrated that blocking EP receptors in T cells during the initial phase of collagen-induced arthritis in mice resulted in a reduction of clinical arthritis. This could be attributable to defective T-cell activation, accompanied by a decline in activated and interferon-γ-producing CD4 + Th1 cells in draining LNs. In conclusion, we prove that T lymphocytes secret picomolar concentrations of PGE 2, which in turn provide additive co-stimulatory signaling, enabling T cells to attain a favorable activation threshold. PGE 2 signaling in T cells is also required for maintaining long and stable interactions with DCs within LNs. Blockade of EP receptors in vivo impairs T-cell activation and development of T cell-mediated inflammatory responses. This may have implications in various pathophysiological settings.},
author = {Sreeramkumar, Vinatha and Hons, Miroslav and Punzón, Carmen and Stein, Jens and Sancho, David and Fresno Forcelledo, Manuel and Cuesta, Natalia},
journal = {Immunology and Cell Biology},
number = {1},
pages = {39 -- 51},
publisher = {Nature Publishing Group},
title = {{Efficient T-cell priming and activation requires signaling through prostaglandin E2 (EP) receptors}},
doi = {10.1038/icb.2015.62},
volume = {94},
year = {2016},
}
@article{1218,
abstract = {Investigating the physiology of cyanobacteria cultured under a diel light regime is relevant for a better understanding of the resulting growth characteristics and for specific biotechnological applications that are foreseen for these photosynthetic organisms. Here, we present the results of a multiomics study of the model cyanobacterium Synechocystis sp. strain PCC 6803, cultured in a lab-scale photobioreactor in physiological conditions relevant for large-scale culturing. The culture was sparged withN2 andCO2, leading to an anoxic environment during the dark period. Growth followed the availability of light. Metabolite analysis performed with 1Hnuclear magnetic resonance analysis showed that amino acids involved in nitrogen and sulfur assimilation showed elevated levels in the light. Most protein levels, analyzed through mass spectrometry, remained rather stable. However, several high-light-response proteins and stress-response proteins showed distinct changes at the onset of the light period. Microarray-based transcript analysis found common patterns of~56% of the transcriptome following the diel regime. These oscillating transcripts could be grouped coarsely into genes that were upregulated and downregulated in the dark period. The accumulated glycogen was degraded in the anaerobic environment in the dark. A small part was degraded gradually, reflecting basic maintenance requirements of the cells in darkness. Surprisingly, the largest part was degraded rapidly in a short time span at the end of the dark period. This degradation could allow rapid formation of metabolic intermediates at the end of the dark period, preparing the cells for the resumption of growth at the start of the light period.},
author = {Angermayr, Andreas and Van Alphen, Pascal and Hasdemir, Dicle and Kramer, Gertjan and Iqbal, Muzamal and Van Grondelle, Wilmar and Hoefsloot, Huub and Choi, Younghae and Hellingwerf, Klaas},
journal = {Applied and Environmental Microbiology},
number = {14},
pages = {4180 -- 4189},
publisher = {American Society for Microbiology},
title = {{Culturing synechocystis sp. Strain pcc 6803 with N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with low maintenance costs}},
doi = {10.1128/AEM.00256-16},
volume = {82},
year = {2016},
}
@article{1219,
abstract = {We consider N×N random matrices of the form H = W + V where W is a real symmetric or complex Hermitian Wigner matrix and V is a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W, and we choose V so that the eigenvalues ofW and V are typically of the same order. For a large class of diagonal matrices V , we show that the local statistics in the bulk of the spectrum are universal in the limit of large N.},
author = {Lee, Jioon and Schnelli, Kevin and Stetler, Ben and Yau, Horngtzer},
journal = {Annals of Probability},
number = {3},
pages = {2349 -- 2425},
publisher = {Institute of Mathematical Statistics},
title = {{Bulk universality for deformed wigner matrices}},
doi = {10.1214/15-AOP1023},
volume = {44},
year = {2016},
}
@article{122,
abstract = {Four rigid panels connected by hinges that meet at a point form a four-vertex, the fundamental building block of origami metamaterials. Most materials designed so far are based on the same four-vertex geometry, and little is known regarding how different geometries affect folding behavior. Here we systematically categorize and analyze the geometries and resulting folding motions of Euclidean four-vertices. Comparing the relative sizes of sector angles, we identify three types of generic vertices and two accompanying subtypes. We determine which folds can fully close and the possible mountain-valley assignments. Next, we consider what occurs when sector angles or sums thereof are set equal, which results in 16 special vertex types. One of these, flat-foldable vertices, has been studied extensively, but we show that a wide variety of qualitatively different folding motions exist for the other 15 special and 3 generic types. Our work establishes a straightforward set of rules for understanding the folding motion of both generic and special four-vertices and serves as a roadmap for designing origami metamaterials.},
author = {Waitukaitis, Scott R and Van Hecke, Martin},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
number = {2},
publisher = {American Physiological Society},
title = {{Origami building blocks: Generic and special four-vertices}},
doi = {10.1103/PhysRevE.93.023003},
volume = {93},
year = {2016},
}
@inproceedings{1220,
abstract = {Theoretical and numerical aspects of aerodynamic efficiency of propulsion systems coupled to the boundary layer of a fuselage are studied. We discuss the effects of local flow fields, which are affected both by conservative flow acceleration as well as total pressure losses, on the efficiency of boundary layer immersed propulsion devices. We introduce the concept of a boundary layer retardation turbine that helps reduce skin friction over the fuselage. We numerically investigate efficiency gains offered by boundary layer and wake interacting devices. We discuss the results in terms of a total energy consumption framework and show that efficiency gains of any device depend on all the other elements of the propulsion system.},
author = {Mikić, Gregor and Stoll, Alex and Bevirt, Joe and Grah, Rok and Moore, Mark},
location = {Washington, D.C., USA},
pages = {1 -- 19},
publisher = {AIAA},
title = {{Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency}},
doi = {10.2514/6.2016-3764},
year = {2016},
}
@article{1221,
abstract = {The Auxin Binding Protein 1 (ABP1) is one of the most studied proteins in plants. Since decades ago, it has been the prime receptor candidate for the plant hormone auxin with a plethora of described functions in auxin signaling and development. The developmental importance of ABP1 has recently been questioned by identification of Arabidopsis thaliana abp1 knock-out alleles that show no obvious phenotypes under normal growth conditions. In this study, we examined the contradiction between the normal growth and development of the abp1 knock-outs and the strong morphological defects observed in three different ethanol-inducible abp1 knock-down mutants ( abp1-AS, SS12K, SS12S). By analyzing segregating populations of abp1 knock-out vs. abp1 knock-down crosses we show that the strong morphological defects that were believed to be the result of conditional down-regulation of ABP1 can be reproduced also in the absence of the functional ABP1 protein. This data suggests that the phenotypes in abp1 knock-down lines are due to the off-target effects and asks for further reflections on the biological function of ABP1 or alternative explanations for the missing phenotypic defects in the abp1 loss-of-function alleles.},
author = {Michalko, Jaroslav and Glanc, Matous and Perrot Rechenmann, Catherine and Friml, Jirí},
journal = {F1000 Research },
publisher = {F1000 Research Ltd. },
title = {{Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein}},
doi = {10.12688/f1000research.7654.1},
volume = {5},
year = {2016},
}
@article{1222,
abstract = {We consider packings of congruent circles on a square flat torus, i.e., periodic (w.r.t. a square lattice) planar circle packings, with the maximal circle radius. This problem is interesting due to a practical reason—the problem of “super resolution of images.” We have found optimal arrangements for N=6, 7 and 8 circles. Surprisingly, for the case N=7 there are three different optimal arrangements. Our proof is based on a computer enumeration of toroidal irreducible contact graphs.},
author = {Musin, Oleg and Nikitenko, Anton},
journal = {Discrete & Computational Geometry},
number = {1},
pages = {1 -- 20},
publisher = {Springer},
title = {{Optimal packings of congruent circles on a square flat torus}},
doi = {10.1007/s00454-015-9742-6},
volume = {55},
year = {2016},
}
@article{1223,
abstract = {We consider a random Schrödinger operator on the binary tree with a random potential which is the sum of a random radially symmetric potential, Qr, and a random transversally periodic potential, κQt, with coupling constant κ. Using a new one-dimensional dynamical systems approach combined with Jensen's inequality in hyperbolic space (our key estimate) we obtain a fractional moment estimate proving localization for small and large κ. Together with a previous result we therefore obtain a model with two Anderson transitions, from localization to delocalization and back to localization, when increasing κ. As a by-product we also have a partially new proof of one-dimensional Anderson localization at any disorder.},
author = {Froese, Richard and Lee, Darrick and Sadel, Christian and Spitzer, Wolfgang and Stolz, Günter},
journal = {Journal of Spectral Theory},
number = {3},
pages = {557 -- 600},
publisher = {European Mathematical Society},
title = {{Localization for transversally periodic random potentials on binary trees}},
doi = {10.4171/JST/132},
volume = {6},
year = {2016},
}
@article{1224,
abstract = {Sexual dimorphism in resource allocation is expected to change during the life cycle of dioecious plants because of temporal differences between the sexes in reproductive investment. Given the potential for sex-specific differences in reproductive costs, resource availability may contribute to variation in reproductive allocation in females and males. Here, we used Rumex hastatulus, a dioecious, wind-pollinated annual plant, to investigate whether sexual dimorphism varies with life-history stage and nutrient availability, and determine whether allocation patterns differ depending on reproductive commitment. To examine if the costs of reproduction varied between the sexes, reproduction was either allowed or prevented through bud removal, and biomass allocation was measured at maturity. In a second experiment to assess variation in sexual dimorphism across the life cycle, and whether this varied with resource availability, plants were grown in high and low nutrients and allocation to roots, aboveground vegetative growth and reproduction were measured at three developmental stages. Males prevented from reproducing compensated with increased above- and belowground allocation to a much larger degree than females, suggesting that male reproductive costs reduce vegetative growth. The proportional allocation to roots, reproductive structures and aboveground vegetative growth varied between the sexes and among life-cycle stages, but not with nutrient treatment. Females allocated proportionally more resources to roots than males at peak flowering, but this pattern was reversed at reproductive maturity under low-nutrient conditions. Our study illustrates the importance of temporal dynamics in sex-specific resource allocation and provides support for high male reproductive costs in wind-pollinated plants.},
author = {Teitel, Zachary and Pickup, Melinda and Field, David and Barrett, Spencer},
journal = {Plant Biology},
number = {1},
pages = {98 -- 103},
publisher = {Wiley-Blackwell},
title = {{The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant}},
doi = {10.1111/plb.12336},
volume = {18},
year = {2016},
}
@inproceedings{1225,
abstract = {At Crypto 2015 Fuchsbauer, Hanser and Slamanig (FHS) presented the first standard-model construction of efficient roundoptimal blind signatures that does not require complexity leveraging. It is conceptually simple and builds on the primitive of structure-preserving signatures on equivalence classes (SPS-EQ). FHS prove the unforgeability of their scheme assuming EUF-CMA security of the SPS-EQ scheme and hardness of a version of the DH inversion problem. Blindness under adversarially chosen keys is proven under an interactive variant of the DDH assumption. We propose a variant of their scheme whose blindness can be proven under a non-interactive assumption, namely a variant of the bilinear DDH assumption. We moreover prove its unforgeability assuming only unforgeability of the underlying SPS-EQ but no additional assumptions as needed for the FHS scheme.},
author = {Fuchsbauer, Georg and Hanser, Christian and Kamath Hosdurg, Chethan and Slamanig, Daniel},
location = {Amalfi, Italy},
pages = {391 -- 408},
publisher = {Springer},
title = {{Practical round-optimal blind signatures in the standard model from weaker assumptions}},
doi = {10.1007/978-3-319-44618-9_21},
volume = {9841},
year = {2016},
}
@article{1226,
abstract = {Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation. Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. We observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active-deactive transition of the enzyme. Our structure provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations.},
author = {Fiedorczuk, Karol and Letts, James A and Degliesposti, Gianluca and Kaszuba, Karol and Skehel, Mark and Sazanov, Leonid A},
journal = {Nature},
number = {7625},
pages = {406 -- 410},
publisher = {Nature Publishing Group},
title = {{Atomic structure of the entire mammalian mitochondrial complex i}},
doi = {10.1038/nature19794},
volume = {538},
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{1229,
abstract = {Witness encryption (WE) was introduced by Garg et al. [GGSW13]. A WE scheme is defined for some NP language L and lets a sender encrypt messages relative to instances x. A ciphertext for x can be decrypted using w witnessing x ∈ L, but hides the message if x ∈ L. Garg et al. construct WE from multilinear maps and give another construction [GGH+13b] using indistinguishability obfuscation (iO) for circuits. Due to the reliance on such heavy tools, WE can cur- rently hardly be implemented on powerful hardware and will unlikely be realizable on constrained devices like smart cards any time soon. We construct a WE scheme where encryption is done by simply computing a Naor-Yung ciphertext (two CPA encryptions and a NIZK proof). To achieve this, our scheme has a setup phase, which outputs public parameters containing an obfuscated circuit (only required for decryption), two encryption keys and a common reference string (used for encryption). This setup need only be run once, and the parame- ters can be used for arbitrary many encryptions. Our scheme can also be turned into a functional WE scheme, where a message is encrypted w.r.t. a statement and a function f, and decryption with a witness w yields f (m, w). Our construction is inspired by the functional encryption scheme by Garg et al. and we prove (selective) security assuming iO and statistically simulation-sound NIZK. We give a construction of the latter in bilinear groups and combining it with ElGamal encryption, our ciphertexts are of size 1.3 kB at a 128-bit security level and can be computed on a smart card.},
author = {Abusalah, Hamza M and Fuchsbauer, Georg and Pietrzak, Krzysztof Z},
location = {Guildford, UK},
pages = {285 -- 303},
publisher = {Springer},
title = {{Offline witness encryption}},
doi = {10.1007/978-3-319-39555-5_16},
volume = {9696},
year = {2016},
}
@inproceedings{1230,
abstract = {Concolic testing is a promising method for generating test suites for large programs. However, it suffers from the path-explosion problem and often fails to find tests that cover difficult-to-reach parts of programs. In contrast, model checkers based on counterexample-guided abstraction refinement explore programs exhaustively, while failing to scale on large programs with precision. In this paper, we present a novel method that iteratively combines concolic testing and model checking to find a test suite for a given coverage criterion. If concolic testing fails to cover some test goals, then the model checker refines its program abstraction to prove more paths infeasible, which reduces the search space for concolic testing. We have implemented our method on top of the concolictesting tool Crest and the model checker CpaChecker. We evaluated our tool on a collection of programs and a category of SvComp benchmarks. In our experiments, we observed an improvement in branch coverage compared to Crest from 48% to 63% in the best case, and from 66% to 71% on average.},
author = {Daca, Przemyslaw and Gupta, Ashutosh and Henzinger, Thomas A},
location = {St. Petersburg, FL, USA},
pages = {328 -- 347},
publisher = {Springer},
title = {{Abstraction-driven concolic testing}},
doi = {10.1007/978-3-662-49122-5_16},
volume = {9583},
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{1234,
abstract = {We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds.},
author = {Daca, Przemyslaw and Henzinger, Thomas A and Kretinsky, Jan and Petrov, Tatjana},
location = {Eindhoven, The Netherlands},
pages = {112 -- 129},
publisher = {Springer},
title = {{Faster statistical model checking for unbounded temporal properties}},
doi = {10.1007/978-3-662-49674-9_7},
volume = {9636},
year = {2016},
}
@inproceedings{1235,
abstract = {A constrained pseudorandom function (CPRF) F: K×X → Y for a family T of subsets of χ is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a short constrained key kS, which allows to evaluate F(k, ·) on all inputs x ∈ S, while the outputs on all inputs x /∈ S look random even given kS. Abusalah et al. recently constructed the first constrained PRF for inputs of arbitrary length whose sets S are decided by Turing machines. They use their CPRF to build broadcast encryption and the first ID-based non-interactive key exchange for an unbounded number of users. Their constrained keys are obfuscated circuits and are therefore large. In this work we drastically reduce the key size and define a constrained key for a Turing machine M as a short signature on M. For this, we introduce a new signature primitive with constrained signing keys that let one only sign certain messages, while forging a signature on others is hard even when knowing the coins for key generation.},
author = {Abusalah, Hamza M and Fuchsbauer, Georg},
location = {Guildford, UK},
pages = {445 -- 463},
publisher = {Springer},
title = {{Constrained PRFs for unbounded inputs with short keys}},
doi = {10.1007/978-3-319-39555-5_24},
volume = {9696},
year = {2016},
}
@inproceedings{1236,
abstract = {A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13 Boneh and Waters gave a construction which supports the most general set family so far. Its keys kc are defined for sets decided by boolean circuits C and enable evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF input length and the size of the circuits C for which constrained keys can be computed must be fixed beforehand during key generation. We construct a constrained PRF that has an unbounded input length and whose constrained keys can be defined for any set recognized by a Turing machine. The only a priori bound we make is on the description size of the machines. We prove our construction secure assuming publiccoin differing-input obfuscation. As applications of our constrained PRF we build a broadcast encryption scheme where the number of potential receivers need not be fixed at setup (in particular, the length of the keys is independent of the number of parties) and the first identity-based non-interactive key exchange protocol with no bound on the number of parties that can agree on a shared key.},
author = {Abusalah, Hamza M and Fuchsbauer, Georg and Pietrzak, Krzysztof Z},
location = {San Francisco, CA, USA},
pages = {413 -- 428},
publisher = {Springer},
title = {{Constrained PRFs for unbounded inputs}},
doi = {10.1007/978-3-319-29485-8_24},
volume = {9610},
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 > 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},
}
@article{1243,
abstract = {Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of self/non-self discrimination in prokaryotes [1], which protects hosts from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase (M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by methylating short specific DNA sequences called restriction sites, whereas R recognizes unmethylated restriction sites as non-self and introduces a double-stranded DNA break [3]. Restriction sites are significantly underrepresented in prokaryotic genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote DNA recombination [9] and contribute to genetic variation in microbial populations, thus facilitating adaptive evolution [10]. However, cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has not been directly detected, and its cause, frequency, and outcome are unknown. We quantify self-restriction caused by two RM systems of Escherichia coli and find that, in agreement with levels of restriction site avoidance, EcoRI, but not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process, which temporarily induces the SOS response, and is followed by DNA repair, maintaining cell viability. We find that RM systems with higher restriction efficiency against bacteriophage infections exhibit a higher rate of self-restriction, and that this rate can be further increased by stochastic imbalance between R and M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic genomes.},
author = {Pleska, Maros and Qian, Long and Okura, Reiko and Bergmiller, Tobias and Wakamoto, Yuichi and Kussell, Edo and Guet, Calin C},
journal = {Current Biology},
number = {3},
pages = {404 -- 409},
publisher = {Cell Press},
title = {{Bacterial autoimmunity due to a restriction-modification system}},
doi = {10.1016/j.cub.2015.12.041},
volume = {26},
year = {2016},
}