@phdthesis{1128,
  abstract     = {The process of gene expression is central to the modern understanding of how cellular systems
function. In this process, a special kind of regulatory proteins, called transcription factors,
are important to determine how much protein is produced from a given gene. As biological
information is transmitted from transcription factor concentration to mRNA levels to amounts of
protein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.
This thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical
description of complex promoters responsible for the stochastic production of biomolecules,
(ii) fundamental limits to information processing the cell faces due to the interference from multiple
fluctuating signals, (iii) how the presence of gene expression noise influences the evolution
of regulatory sequences, (iv) and tools for the experimental study of origins and consequences
of cell-cell heterogeneity, including an application to bacterial stress response systems.},
  author       = {Rieckh, Georg},
  issn         = {2663-337X},
  pages        = {114},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Studying the complexities of transcriptional regulation}},
  year         = {2016},
}

@phdthesis{1129,
  abstract     = {Directed cell migration is a hallmark feature, present in almost all multi-cellular
organisms. Despite its importance, basic questions regarding force transduction
or directional sensing are still heavily investigated. Directed migration of cells
guided by immobilized guidance cues - haptotaxis - occurs in key-processes,
such as embryonic development and immunity (Middleton et al., 1997; Nguyen
et al., 2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues
comprise adhesive ligands, such as collagen and fibronectin (Barczyk et al.,
2009), or chemokines - the main guidance cues for migratory leukocytes
(Middleton et al., 1997; Weber et al., 2013). While adhesive ligands serve as
attachment sites guiding cell migration (Carter, 1965), chemokines instruct
haptotactic migration by inducing adhesion to adhesive ligands and directional
guidance (Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis
of the cellular response to immobilized guidance cues requires in vitro assays
that foster cell migration, offer accurate control of the immobilized cues on a
subcellular scale and in the ideal case closely reproduce in vivo conditions. The
exploration of haptotactic cell migration through design and employment of such
assays represents the main focus of this work.
Dendritic cells (DCs) are leukocytes, which after encountering danger
signals such as pathogens in peripheral organs instruct naïve T-cells and
consequently the adaptive immune response in the lymph node (Mellman and
Steinman, 2001). To reach the lymph node from the periphery, DCs follow
haptotactic gradients of the chemokine CCL21 towards lymphatic vessels
(Weber et al., 2013). Questions about how DCs interpret haptotactic CCL21
gradients have not yet been addressed. The main reason for this is the lack of
an assay that offers diverse haptotactic environments, hence allowing the study
of DC migration as a response to different signals of immobilized guidance cue.
In this work, we developed an in vitro assay that enables us to
quantitatively assess DC haptotaxis, by combining precisely controllable
chemokine photo-patterning with physically confining migration conditions. With this tool at hand, we studied the influence of CCL21 gradient properties and
concentration on DC haptotaxis. We found that haptotactic gradient sensing
depends on the absolute CCL21 concentration in combination with the local
steepness of the gradient. Our analysis suggests that the directionality of
migrating DCs is governed by the signal-to-noise ratio of CCL21 binding to its
receptor CCR7. Moreover, the haptotactic CCL21 gradient formed in vivo
provides an optimal shape for DCs to recognize haptotactic guidance cue.
By reconstitution of the CCL21 gradient in vitro we were also able to
study the influence of CCR7 signal termination on DC haptotaxis. To this end,
we used DCs lacking the G-protein coupled receptor kinase GRK6, which is
responsible for CCL21 induced CCR7 receptor phosphorylation and
desensitization (Zidar et al., 2009). We found that CCR7 desensitization by
GRK6 is crucial for maintenance of haptotactic CCL21 gradient sensing in vitro
and confirm those observations in vivo.
In the context of the organism, immobilized haptotactic guidance cues
often coincide and compete with soluble chemotactic guidance cues. During
wound healing, fibroblasts are exposed and influenced by adhesive cues and
soluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,
migrating DCs are exposed to both, soluble chemokines (CCL19 and truncated
CCL21) inducing chemotactic behavior as well as the immobilized CCL21. To
quantitatively assess these complex coinciding immobilized and soluble
guidance cues, we implemented our chemokine photo-patterning technique in a
microfluidic system allowing for chemotactic gradient generation. To validate
the assay, we observed DC migration in competing CCL19/CCL21
environments.
Adhesiveness guided haptotaxis has been studied intensively over the
last century. However, quantitative studies leading to conceptual models are
largely missing, again due to the lack of a precisely controllable in vitro assay. A
requirement for such an in vitro assay is that it must prevent any uncontrolled
cell adhesion. This can be accomplished by stable passivation of the surface. In
addition, controlled adhesion must be sustainable, quantifiable and dose
dependent in order to create homogenous gradients. Therefore, we developed a novel covalent photo-patterning technique satisfying all these needs. In
combination with a sustainable poly-vinyl alcohol (PVA) surface coating we
were able to generate gradients of adhesive cue to direct cell migration. This
approach allowed us to characterize the haptotactic migratory behavior of
zebrafish keratocytes in vitro. Furthermore, defined patterns of adhesive cue
allowed us to control for cell shape and growth on a subcellular scale.},
  author       = {Schwarz, Jan},
  issn         = {2663-337X},
  pages        = {178},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Quantitative analysis of haptotactic cell migration}},
  year         = {2016},
}

@phdthesis{1130,
  abstract     = {In this thesis we present a computer-aided programming approach to concurrency. Our approach helps the programmer by automatically fixing concurrency-related bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are program behaviours that are incorrect w.r.t. a specification. We consider both user-provided explicit specifications in the form of assertion
statements in the code as well as an implicit specification. The implicit specification is inferred from the non-preemptive behaviour. Let us consider sequences of calls that the program makes to an external interface. The implicit specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We consider several semantics-preserving fixes that go beyond atomic sections typically explored in the synchronisation synthesis literature. Our synthesis is able to place locks, barriers and wait-signal statements and last, but not least reorder independent statements. The latter may be useful if a thread is released to early, e.g., before some initialisation is completed. We guarantee that our synthesis does not introduce deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective function. We dub our solution trace-based synchronisation synthesis and it is loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis works by discovering a trace that is incorrect w.r.t. the specification and identifying ordering constraints crucial to trigger the specification violation. Synchronisation may be placed immediately (greedy approach) or delayed until all incorrect traces are found (non-greedy approach). For the non-greedy approach we construct a set of global constraints over synchronisation placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronisation placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronisation solution. We evaluate our approach on a number of realistic (albeit simplified) Linux device-driver
benchmarks. The benchmarks are versions of the drivers with known concurrency-related bugs. For the experiments with an explicit specification we added assertions that would detect the bugs in the experiments. Device drivers lend themselves to implicit specification, where the device and the operating system are the external interfaces. Our experiments demonstrate that our synthesis method is precise and efficient. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronisation placements are produced for our experiments, favouring e.g. a minimal number of synchronisation operations or maximum concurrency.},
  author       = {Tarrach, Thorsten},
  issn         = {2663-337X},
  pages        = {151},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Automatic synthesis of synchronisation primitives for concurrent programs}},
  doi          = {10.15479/at:ista:1130},
  year         = {2016},
}

@phdthesis{1131,
  abstract     = {Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.
In the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).
In the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment.},
  author       = {Tugrul, Murat},
  issn         = {2663-337X},
  pages        = {89},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Evolution of transcriptional regulatory sequences}},
  year         = {2016},
}

@inproceedings{1135,
  abstract     = {Time-triggered (TT) switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. These networks rely on the notion of globally discretized time (i.e. time slots) and a static TT schedule that prescribes which message is sent through which link at every time slot, such that all messages reach their destination before a global timeout. These schedules are generated offline, assuming a static network with fault-free links, and entrusting all error-handling functions to the end user. Assuming the network is static is an over-optimistic view, and indeed links tend to fail in practice. We study synthesis of TT schedules on a network in which links fail over time and we assume the switches run a very simple error-recovery protocol once they detect a crashed link. We address the problem of finding a pk; qresistant schedule; namely, one that, assuming the switches run a fixed error-recovery protocol, guarantees that the number of messages that arrive at their destination by the timeout is at least no matter what sequence of at most k links fail. Thus, we maintain the simplicity of the switches while giving a guarantee on the number of messages that meet the timeout. We show how a pk; q-resistant schedule can be obtained using a CEGAR-like approach: find a schedule, decide whether it is pk; q-resistant, and if it is not, use the witnessing fault sequence to generate a constraint that is added to the program. The newly added constraint disallows the schedule to be regenerated in a future iteration while also eliminating several other schedules that are not pk; q-resistant. We illustrate the applicability of our approach using an SMT-based implementation. © 2016 ACM.},
  author       = {Avni, Guy and Guha, Shibashis and Rodríguez Navas, Guillermo},
  booktitle    = {Proceedings of the 13th International Conference on Embedded Software },
  location     = {Pittsburgh, PA, USA},
  publisher    = {ACM},
  title        = {{Synthesizing time triggered schedules for switched networks with faulty links}},
  doi          = {10.1145/2968478.2968499},
  year         = {2016},
}

@inproceedings{1136,
  abstract     = {We propose an interactive sculpting system for seamlessly editing pre-computed animations of liquid, without the need for any resimulation. The input is a sequence of meshes without correspondences representing the liquid surface over time. Our method enables the efficient selection of consistent space-time parts of this animation, such as moving waves or droplets, which we call space-time features. Once selected, a feature can be copied, edited, or duplicated and then pasted back anywhere in space and time in the same or in another liquid animation sequence. Our method circumvents tedious user interactions by automatically computing the spatial and temporal ranges of the selected feature. We also provide space-time shape editing tools for non-uniform scaling, rotation, trajectory changes, and temporal editing to locally speed up or slow down motion. Using our tools, the user can edit and progressively refine any input simulation result, possibly using a library of precomputed space-time features extracted from other animations. In contrast to the trial-and-error loop usually required to edit animation results through the tuning of indirect simulation parameters, our method gives the user full control over the edited space-time behaviors. © 2016 Copyright held by the owner/author(s).},
  author       = {Manteaux, Pierre and Vimont, Ulysse and Wojtan, Christopher J and Rohmer, Damien and Cani, Marie},
  booktitle    = {Proceedings of the 9th International Conference on Motion in Games },
  location     = {San Francisco, CA, USA},
  publisher    = {ACM},
  title        = {{Space-time sculpting of liquid animation}},
  doi          = {10.1145/2994258.2994261},
  year         = {2016},
}

@article{1137,
  abstract     = {RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency also resulted in defective proliferation, activation and motility of T cells and B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity with defective granule convergence and actin accumulation. Interaction proteomics identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed the migration and activation defects of RASGRP1-deficient lymphocytes.},
  author       = {Salzer, Elisabeth and Çaǧdaş, Deniz and Hons, Miroslav and Mace, Emily and Garncarz, Wojciech and Petronczki, Oezlem and Platzer, René and Pfajfer, Laurène and Bilic, Ivan and Ban, Sol and Willmann, Katharina and Mukherjee, Malini and Supper, Verena and Hsu, Hsiangting and Banerjee, Pinaki and Sinha, Papiya and Mcclanahan, Fabienne and Zlabinger, Gerhard and Pickl, Winfried and Gribben, John and Stockinger, Hannes and Bennett, Keiryn and Huppa, Johannes and Dupré, Loï̈C and Sanal, Özden and Jäger, Ulrich and Sixt, Michael K and Tezcan, Ilhan and Orange, Jordan and Boztug, Kaan},
  journal      = {Nature Immunology},
  number       = {12},
  pages        = {1352 -- 1360},
  publisher    = {Nature Publishing Group},
  title        = {{RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics}},
  doi          = {10.1038/ni.3575},
  volume       = {17},
  year         = {2016},
}

@inproceedings{1138,
  abstract     = {Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider. © 2016 ACM.},
  author       = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
  booktitle    = {Proceedings of the 31st Annual ACM/IEEE Symposium},
  location     = {New York, NY, USA},
  pages        = {76 -- 85},
  publisher    = {IEEE},
  title        = {{Quantitative automata under probabilistic semantics}},
  doi          = {10.1145/2933575.2933588},
  year         = {2016},
}

@inproceedings{1140,
  abstract     = {Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental -regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical -regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. © 2016 ACM.},
  author       = {Chatterjee, Krishnendu and Dvoák, Wolfgang and Henzinger, Monika H and Loitzenbauer, Veronika},
  booktitle    = {Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science},
  location     = {New York, NY, USA},
  pages        = {197 -- 206},
  publisher    = {IEEE},
  title        = {{Model and objective separation with conditional lower bounds: disjunction is harder than conjunction}},
  doi          = {10.1145/2933575.2935304},
  year         = {2016},
}

@article{1142,
  abstract     = {Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders.},
  author       = {Martins, Rui and Maier, Julia and Gorki, Anna and Huber, Kilian and Sharif, Omar and Starkl, Philipp and Saluzzo, Simona and Quattrone, Federica and Gawish, Riem and Lakovits, Karin and Aichinger, Michael and Radic Sarikas, Branka and Lardeau, Charles and Hladik, Anastasiya and Korosec, Ana and Brown, Markus and Vaahtomeri, Kari and Duggan, Michelle and Kerjaschki, Dontscho and Esterbauer, Harald and Colinge, Jacques and Eisenbarth, Stephanie and Decker, Thomas and Bennett, Keiryn and Kubicek, Stefan and Sixt, Michael K and Superti Furga, Giulio and Knapp, Sylvia},
  journal      = {Nature Immunology},
  number       = {12},
  pages        = {1361 -- 1372},
  publisher    = {Nature Publishing Group},
  title        = {{Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions}},
  doi          = {10.1038/ni.3590},
  volume       = {17},
  year         = {2016},
}

@article{1143,
  abstract     = {We study the ground state of a dilute Bose gas in a scaling limit where the Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger functional whose quartic term is proportional to the scattering length of the interparticle interaction potential. We propose a new derivation of this limit problem, with a method that bypasses some of the technical difficulties that previous derivations had to face. The new method is based on a combination of Dyson\'s lemma, the quantum de Finetti theorem and a second moment estimate for ground states of the effective Dyson Hamiltonian. It applies equally well to the case where magnetic fields or rotation are present.},
  author       = {Nam, Phan and Rougerie, Nicolas and Seiringer, Robert},
  journal      = {Analysis and PDE},
  number       = {2},
  pages        = {459 -- 485},
  publisher    = {Mathematical Sciences Publishers},
  title        = {{Ground states of large bosonic systems: The gross Pitaevskii limit revisited}},
  doi          = {10.2140/apde.2016.9.459},
  volume       = {9},
  year         = {2016},
}

@article{1145,
  abstract     = {Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors},
  author       = {Nodzyński, Tomasz and Vanneste, Steffen and Zwiewka, Marta and Pernisová, Markéta and Hejátko, Jan and Friml, Jirí},
  journal      = {Molecular Plant},
  number       = {11},
  pages        = {1504 -- 1519},
  publisher    = {Cell Press},
  title        = {{Enquiry into the topology of plasma membrane localized PIN auxin transport components}},
  doi          = {10.1016/j.molp.2016.08.010},
  volume       = {9},
  year         = {2016},
}

@article{1147,
  abstract     = {Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016.},
  author       = {Balla, Jozef and Medved'Ová, Zuzana and Kalousek, Petr and Matiješčuková, Natálie and Friml, Jirí and Reinöhl, Vilém and Procházka, Stanislav},
  journal      = {Scientific Reports},
  publisher    = {Nature Publishing Group},
  title        = {{Auxin flow mediated competition between axillary buds to restore apical dominance}},
  doi          = {10.1038/srep35955},
  volume       = {6},
  year         = {2016},
}

@article{1151,
  abstract     = {Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al.},
  author       = {Simonini, Sara and Deb, Joyita and Moubayidin, Laila and Stephenson, Pauline and Valluru, Manoj and Freire Rios, Alejandra and Sorefan, Karim and Weijers, Dolf and Friml, Jirí and Östergaard, Lars},
  journal      = {Genes and Development},
  number       = {20},
  pages        = {2286 -- 2296},
  publisher    = {Cold Spring Harbor Laboratory Press},
  title        = {{A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis}},
  doi          = {10.1101/gad.285361.116},
  volume       = {30},
  year         = {2016},
}

@article{1153,
  abstract     = {Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved.},
  author       = {Žádníková, Petra and Wabnik, Krzysztof T and Abuzeineh, Anas and Gallemí, Marçal and Van Der Straeten, Dominique and Smith, Richard and Inze, Dirk and Friml, Jirí and Prusinkiewicz, Przemysław and Benková, Eva},
  journal      = {Plant Cell},
  number       = {10},
  pages        = {2464 -- 2477},
  publisher    = {American Society of Plant Biologists},
  title        = {{A model of differential growth guided apical hook formation in plants}},
  doi          = {10.1105/tpc.15.00569},
  volume       = {28},
  year         = {2016},
}

@article{1154,
  abstract     = {Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. 
},
  author       = {Schwarz, Jan and Bierbaum, Veronika and Merrin, Jack and Frank, Tino and Hauschild, Robert and Bollenbach, Mark Tobias and Tay, Savaş and Sixt, Michael K and Mehling, Matthias},
  journal      = {Scientific Reports},
  publisher    = {Nature Publishing Group},
  title        = {{A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients}},
  doi          = {10.1038/srep36440},
  volume       = {6},
  year         = {2016},
}

@article{1157,
  abstract     = {We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay.},
  author       = {Lee, Ji and Schnelli, Kevin},
  journal      = {Annals of Applied Probability},
  number       = {6},
  pages        = {3786 -- 3839},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population}},
  doi          = {10.1214/16-AAP1193},
  volume       = {26},
  year         = {2016},
}

@article{11574,
  abstract     = {We present new results from the widest narrow-band survey search for Lyα emitters at z = 5.7, just after reionization. We survey a total of 7 deg2 spread over the COSMOS, UDS and SA22 fields. We find over 11 000 line emitters, out of which 514 are robust Lyα candidates at z = 5.7 within a volume of 6.3 × 106 Mpc3. Our Lyα emitters span a wide range in Lyα luminosities, from faint to bright (LLyα ∼ 1042.5–44 erg s−1) and rest-frame equivalent widths (EW0 ∼ 25–1000 Å) in a single, homogeneous data set. By combining all our fields, we find that the faint end slope of the z = 5.7 Lyα luminosity function is very steep, with α=−2.3+0.4−0.3⁠. We also present an updated z = 6.6 Lyα luminosity function, based on comparable volumes and obtained with the same methods, which we directly compare with that at z = 5.7. We find a significant decline of the number density of faint Lyα emitters from z = 5.7 to 6.6 (by 0.5 ± 0.1 dex), but no evolution at the bright end/no evolution in L*. Faint Lyα emitters at z = 6.6 show much more extended haloes than those at z = 5.7, suggesting that neutral Hydrogen plays an important role, increasing the scattering and leading to observations missing faint Lyα emission within the epoch of reionization. Altogether, our results suggest that we are observing patchy reionization which happens first around the brightest Lyα emitters, allowing the number densities of those sources to remain unaffected by the increase of neutral Hydrogen fraction from z ∼ 5 to 7.},
  author       = {Santos, Sérgio and Sobral, David and Matthee, Jorryt J},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift, galaxies: luminosity function, mass function, cosmology: observations, dark ages, reionization, first stars},
  number       = {2},
  pages        = {1678--1691},
  publisher    = {Oxford University Press},
  title        = {{The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization}},
  doi          = {10.1093/mnras/stw2076},
  volume       = {463},
  year         = {2016},
}

@article{11575,
  abstract     = {We investigate correlations between different physical properties of star-forming galaxies in the ‘Evolution and Assembly of GaLaxies and their Environments’ (EAGLE) cosmological hydrodynamical simulation suite over the redshift range 0 ≤ z ≤ 4.5. A principal component analysis reveals that neutral gas fraction (fgas,neutral), stellar mass (Mstellar) and star formation rate (SFR) account for most of the variance seen in the population, with galaxies tracing a two-dimensional, nearly flat, surface in the three-dimensional space of fgas, neutral–Mstellar–SFR with little scatter. The location of this plane varies little with redshift, whereas galaxies themselves move along the plane as their fgas, neutral and SFR drop with redshift. The positions of galaxies along the plane are highly correlated with gas metallicity. The metallicity can therefore be robustly predicted from fgas, neutral, or from the Mstellar and SFR. We argue that the appearance of this ‘Fundamental Plane of star formation’ is a consequence of self-regulation, with the plane's curvature set by the dependence of the SFR on gas density and metallicity. We analyse a large compilation of observations spanning the redshift range 0 ≲ z ≲ 3, and find that such a plane is also present in the data. The properties of the observed Fundamental Plane of star formation are in good agreement with EAGLE's predictions.},
  author       = {Lagos, Claudia del P. and Theuns, Tom and Schaye, Joop and Furlong, Michelle and Bower, Richard G. and Schaller, Matthieu and Crain, Robert A. and Trayford, James W. and Matthee, Jorryt J},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics  stars: formation, ISM: evolution, galaxies: evolution, galaxies: formation, galaxies: ISM},
  number       = {3},
  pages        = {2632--2650},
  publisher    = {Oxford University Press},
  title        = {{The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations}},
  doi          = {10.1093/mnras/stw717},
  volume       = {459},
  year         = {2016},
}

@article{11576,
  abstract     = {We use new near-infrared spectroscopic observations to investigate the nature and evolution of the most luminous Hα emitters at z ∼ 0.8–2.23, which evolve strongly in number density over this period, and compare them to more typical Hα emitters. We study 59 luminous Hα emitters with LHα > L∗Hα⁠, roughly equally split per redshift slice at z ∼ 0.8, 1.47 and 2.23 from the HiZELS and CF-HiZELS surveys. We find that, overall, 30 ± 8 per cent are active galactic nuclei [AGNs; 80 ± 30 per cent of these AGNs are broad-line AGNs, BL-AGNs], and we find little to no evolution in the AGN fraction with redshift, within the errors. However, the AGN fraction increases strongly with Hα luminosity and correlates best with LHα/L∗Hα(z)⁠. While LHα ≤ L∗Hα(z) Hα emitters are largely dominated by star-forming galaxies (>80 per cent), the most luminous Hα emitters (⁠LHα>10L∗Hα(z)⁠) at any cosmic time are essentially all BL-AGN. Using our AGN-decontaminated sample of luminous star-forming galaxies, and integrating down to a fixed Hα luminosity, we find a factor of ∼1300 evolution in the star formation rate density from z = 0 to 2.23. This is much stronger than the evolution from typical Hα star-forming galaxies and in line with the evolution seen for constant luminosity cuts used to select ‘ultraluminous’ infrared galaxies and/or sub-millimetre galaxies. By taking into account the evolution in the typical Hα luminosity, we show that the most strongly star-forming Hα-selected galaxies at any epoch (⁠LHα>L∗Hα(z)⁠) contribute the same fractional amount of ≈15 per cent to the total star formation rate density, at least up to z = 2.23.},
  author       = {Sobral, David and Kohn, Saul A. and Best, Philip N. and Smail, Ian and Harrison, Chris M. and Stott, John and Calhau, João and Matthee, Jorryt J},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: evolution, galaxies: high-redshift, cosmology: observations},
  number       = {2},
  pages        = {1739--1752},
  publisher    = {Oxford University Press},
  title        = {{The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies}},
  doi          = {10.1093/mnras/stw022},
  volume       = {457},
  year         = {2016},
}