@inproceedings{11850, abstract = {Modern networked systems are increasingly reconfigurable, enabling demand-aware infrastructures whose resources can be adjusted according to the workload they currently serve. Such dynamic adjustments can be exploited to improve network utilization and hence performance, by moving frequently interacting communication partners closer, e.g., collocating them in the same server or datacenter. However, dynamically changing the embedding of workloads is algorithmically challenging: communication patterns are often not known ahead of time, but must be learned. During the learning process, overheads related to unnecessary moves (i.e., re-embeddings) should be minimized. This paper studies a fundamental model which captures the tradeoff between the benefits and costs of dynamically collocating communication partners on l servers, in an online manner. Our main contribution is a distributed online algorithm which is asymptotically almost optimal, i.e., almost matches the lower bound (also derived in this paper) on the competitive ratio of any (distributed or centralized) online algorithm.}, author = {Henzinger, Monika H and Neumann, Stefan and Schmid, Stefan}, booktitle = {SIGMETRICS'19: International Conference on Measurement and Modeling of Computer Systems}, isbn = {978-1-4503-6678-6}, location = {Phoenix, AZ, United States}, pages = {43–44}, publisher = {Association for Computing Machinery}, title = {{Efficient distributed workload (re-)embedding}}, doi = {10.1145/3309697.3331503}, year = {2019}, } @inproceedings{11851, abstract = {The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weighted sum of the cut edges. In this paper, we engineer the fastest known exact algorithm for the problem. State-of-the-art algorithms like the algorithm of Padberg and Rinaldi or the algorithm of Nagamochi, Ono and Ibaraki identify edges that can be contracted to reduce the graph size such that at least one minimum cut is maintained in the contracted graph. Our algorithm achieves improvements in running time over these algorithms by a multitude of techniques. First, we use a recently developed fast and parallel inexact minimum cut algorithm to obtain a better bound for the problem. Afterwards, we use reductions that depend on this bound to reduce the size of the graph much faster than previously possible. We use improved data structures to further lower the running time of our algorithm. Additionally, we parallelize the contraction routines of Nagamochi et al. . Overall, we arrive at a system that significantly outperforms the fastest state-of-the-art solvers for the exact minimum cut problem.}, author = {Henzinger, Monika H and Noe, Alexander and Schulz, Christian}, booktitle = {33rd International Parallel and Distributed Processing Symposium}, isbn = {978-1-7281-1247-3}, issn = {1530-2075}, location = {Rio de Janeiro, Brazil}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Shared-memory exact minimum cuts}}, doi = {10.1109/ipdps.2019.00013}, year = {2019}, } @article{15230, abstract = {We have searched the Gaia DR2 catalog for previously unknown hot white dwarfs in the direction of young open star clusters. The aim of this experiment was to try and extend the initial–final mass relation (IFMR) to somewhat higher masses, potentially challenging the Chandrasekhar limit currently thought to be around 1.38 M⊙. We discovered a particularly interesting white dwarf in the direction of the young ∼150 Myr old cluster Messier 47 (NGC 2422). All Gaia indicators (proper motion, parallax, location in the Gaia color–magnitude diagram) suggest that it is a cluster member. Its spectrum, obtained from Gemini-South, yields a number of anomalies: it is a DB (helium-rich atmosphere) white dwarf, it has a large magnetic field (2.5 MG), is of high mass (∼1.06 M⊙), and its colors are very peculiar—particularly the redder ones (r, i, z and y), which suggests that it may have a late-type companion. This may be the only magnetized, detached binary white dwarf with a non-degenerate companion of any spectral type known in or out of a star cluster. If the white dwarf is a cluster member, as all indicators suggest, its progenitor had a mass just over 6 M⊙. It may, however, be telling an even more interesting story than the one related to the IFMR, one about the origin of stellar magnetic fields, SNe I, and gravitational waves from low-mass stellar systems.}, author = {Richer, Harvey B. and Kerr, Ronan and Heyl, Jeremy and Caiazzo, Ilaria and Cummings, Jeffrey and Bergeron, Pierre and Dufour, Patrick}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {2}, publisher = {American Astronomical Society}, title = {{A massive magnetic helium atmosphere white dwarf binary in a young star cluster}}, doi = {10.3847/1538-4357/ab2874}, volume = {880}, year = {2019}, } @article{170, abstract = {Upper and lower bounds, of the expected order of magnitude, are obtained for the number of rational points of bounded height on any quartic del Pezzo surface over ℚ that contains a conic defined over ℚ .}, author = {Browning, Timothy D and Sofos, Efthymios}, journal = {Mathematische Annalen}, number = {3-4}, pages = {977--1016}, publisher = {Springer Nature}, title = {{Counting rational points on quartic del Pezzo surfaces with a rational conic}}, doi = {10.1007/s00208-018-1716-6}, volume = {373}, year = {2019}, } @inbook{5793, abstract = {The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis.}, author = {Asaoka, Yoichi and Morita, Hitoshi and Furumoto, Hiroko and Heisenberg, Carl-Philipp J and Furutani-Seiki, Makoto}, booktitle = {The hippo pathway}, editor = {Hergovich, Alexander}, isbn = {978-1-4939-8909-6}, pages = {167--181}, publisher = {Springer}, title = {{Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids}}, doi = {10.1007/978-1-4939-8910-2_14}, volume = {1893}, year = {2019}, } @article{6023, abstract = {Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.}, author = {Yoshida, Saiko and Van Der Schuren, Alja and Van Dop, Maritza and Van Galen, Luc and Saiga, Shunsuke and Adibi, Milad and Möller, Barbara and Ten Hove, Colette A. and Marhavy, Peter and Smith, Richard and Friml, Jiří and Weijers, Dolf}, journal = {Nature Plants}, number = {2}, pages = {160--166}, publisher = {Springer Nature}, title = {{A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis}}, doi = {10.1038/s41477-019-0363-6}, volume = {5}, year = {2019}, } @misc{6074, abstract = {This dataset contains the supplementary data for the research paper "Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition". The contained files have the following content: 'Supplementary Figures.pdf' Additional figures (as referenced in the paper). 'Supplementary Table 1. Statistics.xlsx' Details on statistical tests performed in the paper. 'Supplementary Table 2. Differentially expressed gene analysis.xlsx' Results for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples. 'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx' Results for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down). 'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx' Results for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant. 'Supplementary Table 5. Cluster identification.xlsx' Results for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories). 'Supplementary Table 6. GO term cluster analysis.xlsx' Results for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1). 'Supplementary Table 7. Setd5 mass spectrometry results.xlsx' Results showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma. 'Supplementary Table 8. PolII ChIP-seq analysis.xlsx' Results for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS.}, author = {Dotter, Christoph and Novarino, Gaia}, publisher = {Institute of Science and Technology Austria}, title = {{Supplementary data for the research paper "Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition"}}, doi = {10.15479/AT:ISTA:6074}, year = {2019}, } @article{6091, abstract = {Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons.}, author = {Henderson, Nathan T. and Le Marchand, Sylvain J. and Hruska, Martin and Hippenmeyer, Simon and Luo, Liqun and Dalva, Matthew B.}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs}}, doi = {10.7554/eLife.41563}, volume = {8}, year = {2019}, } @article{6412, abstract = {Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.}, author = {Moussa, Hagar F. and Bsteh, Daniel and Yelagandula, Ramesh and Pribitzer, Carina and Stecher, Karin and Bartalska, Katarina and Michetti, Luca and Wang, Jingkui and Zepeda-Martinez, Jorge A. and Elling, Ulrich and Stuckey, Jacob I. and James, Lindsey I. and Frye, Stephen V. and Bell, Oliver}, issn = {2041-1723}, journal = {Nature Communications}, number = {1}, publisher = {Springer Nature}, title = {{Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing}}, doi = {10.1038/s41467-019-09628-6}, volume = {10}, year = {2019}, } @article{17924, abstract = {We demonstrate that imidazole based π–π stacked dimers form strong and efficient conductance pathways in single-molecule junctions using the scanning-tunneling microscope-break junction (STM-BJ) technique and density functional theory-based calculations. We first characterize an imidazole-gold contact by measuring the conductance of imidazolyl-terminated alkanes (im-N-im, N = 3–6). We show that the conductance of these alkanes decays exponentially with increasing length, indicating that the mechanism for electron transport is through tunneling or super-exchange. We also reveal that π–π stacked dimers can be formed between imidazoles and have better coupling than through-bond tunneling. These experimental results are rationalized by calculations of molecular junction transmission using non-equilibrium Green's function formalism. This study verifies the capability of imidazole as a Au-binding ligand to form stable single- and π-stacked molecule junctions at room temperature.}, author = {Fu, Tianren and Smith, Shanelle and Camarasa-Gómez, María and Yu, Xiaofang and Xue, Jiayi and Nuckolls, Colin and Evers, Ferdinand and Venkataraman, Latha and Wei, Sujun}, issn = {2041-6539}, journal = {Chemical Science}, number = {43}, pages = {9998--10002}, publisher = {Royal Society of Chemistry}, title = {{Enhanced coupling through π-stacking in imidazole-based molecular junctions}}, doi = {10.1039/c9sc03760h}, volume = {10}, year = {2019}, } @inproceedings{7576, abstract = {We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.}, author = {Immler, Fabian and Althoff, Matthias and Benet, Luis and Chapoutot, Alexandre and Chen, Xin and Forets, Marcelo and Geretti, Luca and Kochdumper, Niklas and Sanders, David P. and Schilling, Christian}, booktitle = {EPiC Series in Computing}, issn = {2398-7340}, location = {Montreal, Canada}, pages = {41--61}, publisher = {EasyChair}, title = {{ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics}}, doi = {10.29007/m75b}, volume = {61}, year = {2019}, } @article{8228, abstract = {Background: Atopics have a lower risk for malignancies, and IgE targeted to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or adaptive immune surveillance can confer protection against tumors remains unclear. Objective: We aimed to investigate the effects of active and passive immunotherapy to the tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor expression affecting the levels of expressed IgE. Methods: We compared the levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b, IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1 mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2 mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy). Results: Overall, among the three strains of mice, HER-2 vaccination induced significantly higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2 mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment controls; active vaccination provided the highest benefit. Notably, untreated high-IgE KN1 mice displayed the longest survival of all strains, which could not be further extended by active or passive immunotherapy. Conclusion: Active and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit following tumor challenge.}, author = {Singer, Josef and Achatz-Straussberger, Gertrude and Bentley-Lukschal, Anna and Fazekas-Singer, Judit and Achatz, Gernot and Karagiannis, Sophia N. and Jensen-Jarolim, Erika}, issn = {1939-4551}, journal = {World Allergy Organization Journal}, number = {7}, publisher = {Elsevier}, title = {{AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice}}, doi = {10.1016/j.waojou.2019.100044}, volume = {12}, year = {2019}, } @article{8263, abstract = {Background: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae. Results: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity. Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism. Conclusions: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.}, author = {Shelyakin, Pavel V. and Bochkareva, Olga and Karan, Anna A. and Gelfand, Mikhail S.}, issn = {1471-2148}, journal = {BMC Evolutionary Biology}, publisher = {Springer Nature}, title = {{Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow}}, doi = {10.1186/s12862-019-1403-6}, volume = {19}, year = {2019}, } @misc{9784, abstract = {Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.}, author = {Antoniou, Michael N. and Nicolas, Armel and Mesnage, Robin and Biserni, Martina and Rao, Francesco V. and Martin, Cristina Vazquez}, publisher = {Springer Nature}, title = {{MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells}}, doi = {10.6084/m9.figshare.9411761.v1}, year = {2019}, } @misc{9805, abstract = {The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?}, author = {Barton, Nicholas H}, publisher = {Dryad}, title = {{Data from: The consequences of an introgression event}}, doi = {10.5061/dryad.2kb6fh4}, year = {2019}, } @inproceedings{6647, abstract = {The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2.}, author = {Fulek, Radoslav and Gärtner, Bernd and Kupavskii, Andrey and Valtr, Pavel and Wagner, Uli}, booktitle = {35th International Symposium on Computational Geometry}, isbn = {9783959771047}, issn = {1868-8969}, location = {Portland, OR, United States}, pages = {38:1--38:13}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The crossing Tverberg theorem}}, doi = {10.4230/LIPICS.SOCG.2019.38}, volume = {129}, year = {2019}, } @article{6819, abstract = {Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.}, author = {Antoniou, Michael N. and Nicolas, Armel and Mesnage, Robin and Biserni, Martina and Rao, Francesco V. and Martin, Cristina Vazquez}, issn = {1756-0500}, journal = {BMC Research Notes}, publisher = {BioMed Central}, title = {{Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells}}, doi = {10.1186/s13104-019-4534-3}, volume = {12}, year = {2019}, } @inproceedings{6933, abstract = {We design fast deterministic algorithms for distance computation in the CONGESTED CLIQUE model. Our key contributions include: - A (2+ε)-approximation for all-pairs shortest paths problem in O(log²n / ε) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model. - A (1+ε)-approximation for multi-source shortest paths problem from O(√n) sources in O(log² n / ε) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size. Our main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in Õ(n^{1/6}) rounds.}, author = {Censor-Hillel, Keren and Dory, Michal and Korhonen, Janne and Leitersdorf, Dean}, booktitle = {Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin}, isbn = {9781450362177}, location = {Toronto, ON, Canada}, pages = {74--83}, publisher = {ACM}, title = {{Fast approximate shortest paths in the congested clique}}, doi = {10.1145/3293611.3331633}, year = {2019}, } @book{7171, abstract = {Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen verbirgt? Dieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens. Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. Ein Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten möchten. Auch für Schülerinnen und Schüler geeignet!}, editor = {Kersting, Kristian and Lampert, Christoph and Rothkopf, Constantin}, isbn = {978-3-658-26762-9}, pages = {XIV, 245}, publisher = {Springer Nature}, title = {{Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt}}, doi = {10.1007/978-3-658-26763-6}, 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 = {1546-1696}, 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}, }