@phdthesis{7172,
  abstract     = {The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.
The first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.
The second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.
The third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.
In the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.
In the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.
In the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes.},
  author       = {Vasileva, Mina K},
  issn         = {2663-337X},
  pages        = {192},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana}},
  doi          = {10.15479/AT:ISTA:7172},
  year         = {2019},
}

@article{7179,
  abstract     = {Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity.},
  author       = {Klotz, Lisa and Wendler, Olaf and Frischknecht, Renato and Shigemoto, Ryuichi and Schulze, Holger and Enz, Ralf},
  issn         = {15306860},
  journal      = {FASEB Journal},
  number       = {12},
  pages        = {13734--13746},
  publisher    = {FASEB},
  title        = {{Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses}},
  doi          = {10.1096/fj.201901543R},
  volume       = {33},
  year         = {2019},
}

@article{7180,
  abstract     = {Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation.},
  author       = {Retzer, Katarzyna and Akhmanova, Maria and Konstantinova, Nataliia and Malínská, Kateřina and Leitner, Johannes and Petrášek, Jan and Luschnig, Christian},
  issn         = {20411723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter}},
  doi          = {10.1038/s41467-019-13543-1},
  volume       = {10},
  year         = {2019},
}

@article{7181,
  abstract     = {Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6.},
  author       = {Garriga, Edgar and Di Tommaso, Paolo and Magis, Cedrik and Erb, Ionas and Mansouri, Leila and Baltzis, Athanasios and Laayouni, Hafid and Kondrashov, Fyodor and Floden, Evan and Notredame, Cedric},
  issn         = {15461696},
  journal      = {Nature Biotechnology},
  number       = {12},
  pages        = {1466--1470},
  publisher    = {Springer Nature},
  title        = {{Large multiple sequence alignments with a root-to-leaf regressive method}},
  doi          = {10.1038/s41587-019-0333-6},
  volume       = {37},
  year         = {2019},
}

@article{7182,
  abstract     = {During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.},
  author       = {Alcântara, André and Bosch, Jason and Nazari, Fahimeh and Hoffmann, Gesa and Gallei, Michelle C and Uhse, Simon and Darino, Martin A. and Olukayode, Toluwase and Reumann, Daniel and Baggaley, Laura and Djamei, Armin},
  issn         = {1664462X},
  journal      = {Frontiers in Plant Science},
  number       = {11},
  publisher    = {Frontiers},
  title        = {{Systematic Y2H screening reveals extensive effector-complex formation}},
  doi          = {10.3389/fpls.2019.01437},
  volume       = {10},
  year         = {2019},
}

@inproceedings{7183,
  abstract     = {A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2).},
  author       = {Brázdil, Tomás and Chatterjee, Krishnendu and Kucera, Antonín and Novotný, Petr and Velan, Dominik},
  booktitle    = {International Symposium on Automated Technology for Verification and Analysis},
  isbn         = {9783030317836},
  issn         = {16113349},
  location     = {Taipei, Taiwan},
  pages        = {462--478},
  publisher    = {Springer Nature},
  title        = {{Deciding fast termination for probabilistic VASS with nondeterminism}},
  doi          = {10.1007/978-3-030-31784-3_27},
  volume       = {11781},
  year         = {2019},
}

@phdthesis{7186,
  abstract     = {Tissue morphogenesis in developmental or physiological processes is regulated by molecular
and mechanical signals. While the molecular signaling cascades are increasingly well
described, the mechanical signals affecting tissue shape changes have only recently been
studied in greater detail. To gain more insight into the mechanochemical and biophysical
basis of an epithelial spreading process (epiboly) in early zebrafish development, we studied
cell-cell junction formation and actomyosin network dynamics at the boundary between
surface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,
the cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of
gastrulation. It has been previously shown that an actomyosin ring residing within the YSL
pulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby
dragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL
actomyosin ring to EVL cells; however, the nature and formation of the junctional structure
mediating this process has not been well described so far. Therefore, our main aim was to
determine the nature, dynamics and potential function of the EVL-YSL junction during this
epithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a
mechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process
of TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated
Zonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we
could demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk
cell, and ZO-1 undergoes a phase separation process that likely renders the protein
responsive to flows. These flows are directed towards the junction and mediate proper
tension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets
incorporated into the junctional pool mediated through its direct actin-binding domain.
When the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their
proper mechanosensitive responses resulting in slower tissue spreading. We could further
demonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin
ring formation. This suggests that a mechanochemical feedback loop is at work during
zebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin
contractility and flows positively influence ZO-1 junctional recruitment. Finally, such a
mesoscale polarization process mediated through the flow of phase-separated protein
clusters might have implications for other processes such as immunological synapse
formation, C. elegans zygote polarization and wound healing.},
  author       = {Schwayer, Cornelia},
  issn         = {2663-337X},
  pages        = {107},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Mechanosensation of tight junctions depends on ZO-1 phase separation and flow}},
  doi          = {10.15479/AT:ISTA:7186},
  year         = {2019},
}

@article{7190,
  abstract     = {We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas.},
  author       = {Huber, D. and Hammer, H.-W. and Volosniev, Artem},
  issn         = {2643-1564},
  journal      = {Physical Review Research},
  number       = {3},
  publisher    = {American Physical Society},
  title        = {{In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas}},
  doi          = {10.1103/physrevresearch.1.033177},
  volume       = {1},
  year         = {2019},
}

@article{7197,
  abstract     = {During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner.},
  author       = {Dos Santos Caldas, Paulo R and Lopez Pelegrin, Maria D and Pearce, Daniel J. G. and Budanur, Nazmi B and Brugués, Jan and Loose, Martin},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA}},
  doi          = {10.1038/s41467-019-13702-4},
  volume       = {10},
  year         = {2019},
}

@article{72,
  abstract     = {We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t.},
  author       = {Ferrari, Patrick and Ghosal, Promit and Nejjar, Peter},
  issn         = {0246-0203},
  journal      = {Annales de l'institut Henri Poincare (B) Probability and Statistics},
  number       = {3},
  pages        = {1203--1225},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Limit law of a second class particle in TASEP with non-random initial condition}},
  doi          = {10.1214/18-AIHP916},
  volume       = {55},
  year         = {2019},
}

@article{7200,
  abstract     = {Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario).},
  author       = {Brighi, Pietro and Grilli, Marco and Leridon, Brigitte and Caprara, Sergio},
  issn         = {2469-9969},
  journal      = {Physical Review B},
  number       = {17},
  publisher    = {American Physical Society},
  title        = {{Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films}},
  doi          = {10.1103/PhysRevB.100.174518},
  volume       = {100},
  year         = {2019},
}

@inproceedings{7201,
  abstract     = {Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed "data parallel" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks.},
  author       = {Renggli, Cedric and Ashkboos, Saleh and Aghagolzadeh, Mehdi and Alistarh, Dan-Adrian and Hoefler, Torsten},
  booktitle    = {International Conference for High Performance Computing, Networking, Storage and Analysis, SC},
  isbn         = {9781450362290},
  issn         = {21674337},
  location     = {Denver, CO, Unites States},
  publisher    = {ACM},
  title        = {{SparCML: High-performance sparse communication for machine learning}},
  doi          = {10.1145/3295500.3356222},
  year         = {2019},
}

@article{7202,
  abstract     = {The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas.},
  author       = {Llorca, Alfredo and Ciceri, Gabriele and Beattie, Robert J and Wong, Fong Kuan and Diana, Giovanni and Serafeimidou-Pouliou, Eleni and Fernández-Otero, Marian and Streicher, Carmen and Arnold, Sebastian J. and Meyer, Martin and Hippenmeyer, Simon and Maravall, Miguel and Marín, Oscar},
  issn         = {2050084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture}},
  doi          = {10.7554/eLife.51381},
  volume       = {8},
  year         = {2019},
}

@article{7210,
  abstract     = {The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these amplifiers of natural selection typically increase fixation time. Here we study population structures that achieve a tradeoff between fixation probability and time. First, we show that no amplifiers can have an asymptotically lower absorption time than the well-mixed population. Then we design population structures that substantially augment the fixation probability with just a minor increase in fixation time. Finally, we show that those structures enable higher effective rate of evolution than the well-mixed population provided that the rate of generating advantageous mutants is relatively low. Our work sheds light on how population structure affects the rate of evolution. Moreover, our structures could be useful for lab-based, medical, or industrial applications of evolutionary optimization.},
  author       = {Tkadlec, Josef and Pavlogiannis, Andreas and Chatterjee, Krishnendu and Nowak, Martin A.},
  issn         = {2399-3642},
  journal      = {Communications Biology},
  publisher    = {Springer Nature},
  title        = {{Population structure determines the tradeoff between fixation probability and fixation time}},
  doi          = {10.1038/s42003-019-0373-y},
  volume       = {2},
  year         = {2019},
}

@article{7214,
  abstract     = {Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.

Results: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.

Conclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.},
  author       = {Aganezov, Sergey and Zban, Ilya and Aksenov, Vitalii and Alexeev, Nikita and Schatz, Michael C.},
  issn         = {14712105},
  journal      = {BMC Bioinformatics},
  publisher    = {BMC},
  title        = {{Recovering rearranged cancer chromosomes from karyotype graphs}},
  doi          = {10.1186/s12859-019-3208-4},
  volume       = {20},
  year         = {2019},
}

@inproceedings{7216,
  abstract     = {We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system to label a stream of noisy observations of transit vehicle trajectories with the transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently to large transit networks, our system first retrieves a small set of candidate routes from a geometrically indexed data structure, then applies a fine-grained scoring step to choose the best match. Given that real-time data remains unavailable for the majority of the world’s transit agencies, these inferences can help feed a real-time map of a transit system’s trips, infer transit trip delays in real time, or measure and correct noisy transit tracking data. This system can run on vehicle observations from a variety of sources that don’t attach route information to vehicle observations, such as public imagery streams or user-contributed transit vehicle sightings.We abstract away the specifics of the sensing system and demonstrate the effectiveness of our system on a "semisynthetic" dataset of all New York City buses, where we simulate sensed trajectories by starting with fully labeled vehicle trajectories reported via the GTFS-Realtime protocol, removing the transit route IDs, and perturbing locations with synthetic noise. Using just the geometric shapes of the trajectories, we demonstrate that our system converges on the correct route ID within a few minutes, even after a vehicle switches from serving one trip to the next.},
  author       = {Osang, Georg F and Cook, James and Fabrikant, Alex and Gruteser, Marco},
  booktitle    = {2019 IEEE Intelligent Transportation Systems Conference},
  isbn         = {9781538670248},
  location     = {Auckland, New Zealand},
  publisher    = {IEEE},
  title        = {{LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale}},
  doi          = {10.1109/ITSC.2019.8917514},
  year         = {2019},
}

@article{7225,
  abstract     = {This is a literature teaching resource review for biologically inspired microfluidics courses
or exploring the diverse applications of microfluidics. The structure is around key papers and model
organisms. While courses gradually change over time, a focus remains on understanding how
microfluidics has developed as well as what it can and cannot do for researchers. As a primary
starting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety
of applications are discussed using model prokaryotic and eukaryotic organisms from the set
of bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),
slime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),
plants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and
biochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,
biotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,
microfluidics can still be used effectively for specific applications.},
  author       = {Merrin, Jack},
  issn         = {23065354},
  journal      = {Bioengineering},
  number       = {4},
  publisher    = {MDPI},
  title        = {{Frontiers in microfluidics, a teaching resource review}},
  doi          = {10.3390/bioengineering6040109},
  volume       = {6},
  year         = {2019},
}

@article{7226,
  author       = {Jaksic, Vojkan and Seiringer, Robert},
  issn         = {00222488},
  journal      = {Journal of Mathematical Physics},
  number       = {12},
  publisher    = {AIP Publishing},
  title        = {{Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018}},
  doi          = {10.1063/1.5138135},
  volume       = {60},
  year         = {2019},
}

@inproceedings{7228,
  abstract     = {Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) and actor models, which share data via explicit communication. These models have been known for almost half a century, and have recently had started to gain significant traction among modern programming languages. The common abstraction for communication between several processes is the channel. Although channels are similar to producer-consumer data structures, they have different semantics and support additional operations, such as the select expression. Despite their growing popularity, most known implementations of channels use lock-based data structures and can be rather inefficient.

In this paper, we present the first efficient lock-free algorithm for implementing a communication channel for CSP programming. We provide implementations and experimental results in the Kotlin and Go programming languages. Our new algorithm outperforms existing implementations on many workloads, while providing non-blocking progress guarantee. Our design can serve as an example of how to construct general communication data structures for CSP and actor models. },
  author       = {Koval, Nikita and Alistarh, Dan-Adrian and Elizarov, Roman},
  booktitle    = {25th Anniversary of Euro-Par},
  isbn         = {978-3-0302-9399-4},
  issn         = {1611-3349},
  location     = {Göttingen, Germany},
  pages        = {317--333},
  publisher    = {Springer Nature},
  title        = {{Scalable FIFO channels for programming via communicating sequential processes}},
  doi          = {10.1007/978-3-030-29400-7_23},
  volume       = {11725},
  year         = {2019},
}

@inproceedings{7230,
  abstract     = {Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G.},
  author       = {Arroyo Guevara, Alan M and Derka, Martin and Parada, Irene},
  booktitle    = {27th International Symposium on Graph Drawing and Network Visualization},
  isbn         = {978-3-0303-5801-3},
  issn         = {1611-3349},
  location     = {Prague, Czech Republic},
  pages        = {230--243},
  publisher    = {Springer Nature},
  title        = {{Extending simple drawings}},
  doi          = {10.1007/978-3-030-35802-0_18},
  volume       = {11904},
  year         = {2019},
}