@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{6822, abstract = {In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the qualitative winner or quantitative payoff of the game. In bidding games, in each turn, we hold an auction between the two players to determine which player moves the token. Bidding games have largely been studied with concrete bidding mechanisms that are variants of a first-price auction: in each turn both players simultaneously submit bids, the higher bidder moves the token, and pays his bid to the lower bidder in Richman bidding, to the bank in poorman bidding, and in taxman bidding, the bid is split between the other player and the bank according to a predefined constant factor. Bidding games are deterministic games. They have an intriguing connection with a fragment of stochastic games called randomturn games. We study, for the first time, a combination of bidding games with probabilistic behavior; namely, we study bidding games that are played on Markov decision processes, where the players bid for the right to choose the next action, which determines the probability distribution according to which the next vertex is chosen. We study parity and meanpayoff bidding games on MDPs and extend results from the deterministic bidding setting to the probabilistic one.}, author = {Avni, Guy and Henzinger, Thomas A and Ibsen-Jensen, Rasmus and Novotny, Petr}, booktitle = { Proceedings of the 13th International Conference of Reachability Problems}, isbn = {978-303030805-6}, issn = {0302-9743}, location = {Brussels, Belgium}, pages = {1--12}, publisher = {Springer}, title = {{Bidding games on Markov decision processes}}, doi = {10.1007/978-3-030-30806-3_1}, volume = {11674}, 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}, } @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}, } @misc{9897, abstract = {Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes. Only 374 genes with typical length and domain composition were considered. (CSV 6 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808850.v1}, year = {2019}, } @article{10874, abstract = {In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM.}, author = {Ionica, Sorina and Kılıçer, Pınar and Lauter, Kristin and Lorenzo García, Elisa and Manzateanu, Maria-Adelina and Massierer, Maike and Vincent, Christelle}, issn = {2363-9555}, journal = {Research in Number Theory}, keywords = {Algebra and Number Theory}, publisher = {Springer Nature}, title = {{Modular invariants for genus 3 hyperelliptic curves}}, doi = {10.1007/s40993-018-0146-6}, volume = {5}, year = {2019}, } @article{11505, abstract = {Contact. This paper presents the results obtained with the Multi-Unit Spectroscopic Explorer (MUSE) at the ESO Very Large Telescope on the faint end of the Lyman-alpha luminosity function (LF) based on deep observations of four lensing clusters. The goal of our project is to set strong constraints on the relative contribution of the Lyman-alpha emitter (LAE) population to cosmic reionization. Aims. The precise aim of the present study is to further constrain the abundance of LAEs by taking advantage of the magnification provided by lensing clusters to build a blindly selected sample of galaxies which is less biased than current blank field samples in redshift and luminosity. By construction, this sample of LAEs is complementary to those built from deep blank fields, whether observed by MUSE or by other facilities, and makes it possible to determine the shape of the LF at fainter levels, as well as its evolution with redshift. Methods. We selected a sample of 156 LAEs with redshifts between 2.9 ≤ z ≤ 6.7 and magnification-corrected luminosities in the range 39 ≲ log LLyα [erg s−1] ≲43. To properly take into account the individual differences in detection conditions between the LAEs when computing the LF, including lensing configurations, and spatial and spectral morphologies, the non-parametric 1/Vmax method was adopted. The price to pay to benefit from magnification is a reduction of the effective volume of the survey, together with a more complex analysis procedure to properly determine the effective volume Vmax for each galaxy. In this paper we present a complete procedure for the determination of the LF based on IFU detections in lensing clusters. This procedure, including some new methods for masking, effective volume integration and (individual) completeness determinations, has been fully automated when possible, and it can be easily generalized to the analysis of IFU observations in blank fields. Results. As a result of this analysis, the Lyman-alpha LF has been obtained in four different redshift bins: 2.9 <  z <  6, 7, 2.9 <  z <  4.0, 4.0 <  z <  5.0, and 5.0 <  z <  6.7 with constraints down to log LLyα = 40.5. From our data only, no significant evolution of LF mean slope can be found. When performing a Schechter analysis also including data from the literature to complete the present sample towards the brightest luminosities, a steep faint end slope was measured varying from α = −1.69−0.08+0.08 to α = −1.87−0.12+0.12 between the lowest and the highest redshift bins. Conclusions. The contribution of the LAE population to the star formation rate density at z ∼ 6 is ≲50% depending on the luminosity limit considered, which is of the same order as the Lyman-break galaxy (LBG) contribution. The evolution of the LAE contribution with redshift depends on the assumed escape fraction of Lyman-alpha photons, and appears to slightly increase with increasing redshift when this fraction is conservatively set to one. Depending on the intersection between the LAE/LBG populations, the contribution of the observed galaxies to the ionizing flux may suffice to keep the universe ionized at z ∼ 6.}, author = {de La Vieuville, G. and Bina, D. and Pello, R. and Mahler, G. and Richard, J. and Drake, A. B. and Herenz, E. C. and Bauer, F. E. and Clément, B. and Lagattuta, D. and Laporte, N. and Martinez, J. and Patrício, V. and Wisotzki, L. and Zabl, J. and Bouwens, R. J. and Contini, T. and Garel, T. and Guiderdoni, B. and Marino, R. A. and Maseda, M. V. and Matthee, Jorryt J and Schaye, J. and Soucail, G.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, gravitational lensing: strong / galaxies: high-redshift / dark ages, reionization, first stars / galaxies: clusters: general / galaxies: luminosity function, mass function}, publisher = {EDP Sciences}, title = {{Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE}}, doi = {10.1051/0004-6361/201834471}, volume = {628}, year = {2019}, } @article{11535, abstract = {We investigate the clustering and halo properties of ∼5000 Ly α-selected emission-line galaxies (LAEs) from the Slicing COSMOS 4K (SC4K) and from archival NB497 imaging of SA22 split in 15 discrete redshift slices between z ∼ 2.5 and 6. We measure clustering lengths of r0 ∼ 3–6 h−1 Mpc and typical halo masses of ∼1011 M⊙ for our narrowband-selected LAEs with typical LLy α ∼ 1042–43 erg s−1. The intermediate-band-selected LAEs are observed to have r0 ∼ 3.5–15 h−1 Mpc with typical halo masses of ∼1011–12 M⊙ and typical LLy α ∼ 1043–43.6 erg s−1. We find a strong, redshift-independent correlation between halo mass and Ly α luminosity normalized by the characteristic Ly α luminosity, L⋆(z). The faintest LAEs (L ∼ 0.1 L⋆(z)) typically identified by deep narrowband surveys are found in 1010 M⊙ haloes and the brightest LAEs (L ∼ 7 L⋆(z)) are found in ∼5 × 1012 M⊙ haloes. A dependency on the rest-frame 1500 Å UV luminosity, MUV, is also observed where the halo masses increase from 1011 to 1013 M⊙ for MUV ∼ −19 to −23.5 mag. Halo mass is also observed to increase from 109.8 to 1012 M⊙ for dust-corrected UV star formation rates from ∼0.6 to 10 M⊙ yr−1 and continues to increase up to 1013 M⊙ in halo mass, where the majority of those sources are active galactic nuclei. All the trends we observe are found to be redshift independent. Our results reveal that LAEs are the likely progenitors of a wide range of galaxies depending on their luminosity, from dwarf-like, to Milky Way-type, to bright cluster galaxies. LAEs therefore provide unique insight into the early formation and evolution of the galaxies we observe in the local Universe.}, author = {Khostovan, A A and Sobral, D and Mobasher, B and Matthee, Jorryt J and Cochrane, R K and Chartab, N and Jafariyazani, M and Paulino-Afonso, A and Santos, S and Calhau, J}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: evolution, galaxies: haloes, galaxies: high-redshift, galaxies: star formation, cosmology: observations, large-scale structure of Universe}, number = {1}, pages = {555--573}, publisher = {Oxford University Press}, title = {{The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities}}, doi = {10.1093/mnras/stz2149}, volume = {489}, year = {2019}, } @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}, } @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}, } @article{76, abstract = {Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.}, author = {Lenzen, Christoph and Rybicki, Joel}, journal = {Distributed Computing}, publisher = {Springer}, title = {{Near-optimal self-stabilising counting and firing squads}}, doi = {10.1007/s00446-018-0342-6}, year = {2018}, } @article{7713, abstract = {There are mean differences in complex traits among global human populations. We hypothesize that part of the phenotypic differentiation is due to natural selection. To address this hypothesis, we assess the differentiation in allele frequencies of trait-associated SNPs among African, Eastern Asian, and European populations for ten complex traits using data of large sample size (up to ~405,000). We show that SNPs associated with height (P=2.46×10−5), waist-to-hip ratio (P=2.77×10−4), and schizophrenia (P=3.96×10−5) are significantly more differentiated among populations than matched “control” SNPs, suggesting that these trait-associated SNPs have undergone natural selection. We further find that SNPs associated with height (P=2.01×10−6) and schizophrenia (P=5.16×10−18) show significantly higher variance in linkage disequilibrium (LD) scores across populations than control SNPs. Our results support the hypothesis that natural selection has shaped the genetic differentiation of complex traits, such as height and schizophrenia, among worldwide populations.}, author = {Guo, Jing and Wu, Yang and Zhu, Zhihong and Zheng, Zhili and Trzaskowski, Maciej and Zeng, Jian and Robinson, Matthew Richard and Visscher, Peter M. and Yang, Jian}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Global genetic differentiation of complex traits shaped by natural selection in humans}}, doi = {10.1038/s41467-018-04191-y}, volume = {9}, year = {2018}, } @article{7716, abstract = {Genomic prediction has the potential to contribute to precision medicine. However, to date, the utility of such predictors is limited due to low accuracy for most traits. Here theory and simulation study are used to demonstrate that widespread pleiotropy among phenotypes can be utilised to improve genomic risk prediction. We show how a genetic predictor can be created as a weighted index that combines published genome-wide association study (GWAS) summary statistics across many different traits. We apply this framework to predict risk of schizophrenia and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial heterogeneity in prediction accuracy increases across cohorts. For six additional phenotypes in the UK Biobank data, we find increases in prediction accuracy ranging from 0.7% for height to 47% for type 2 diabetes, when using a multi-trait predictor that combines published summary statistics from multiple traits, as compared to a predictor based only on one trait.}, author = {Maier, Robert M. and Zhu, Zhihong and Lee, Sang Hong and Trzaskowski, Maciej and Ruderfer, Douglas M. and Stahl, Eli A. and Ripke, Stephan and Wray, Naomi R. and Yang, Jian and Visscher, Peter M. and Robinson, Matthew Richard}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Improving genetic prediction by leveraging genetic correlations among human diseases and traits}}, doi = {10.1038/s41467-017-02769-6}, volume = {9}, year = {2018}, } @article{7722, abstract = {We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits.}, author = {Zeng, Jian and de Vlaming, Ronald and Wu, Yang and Robinson, Matthew Richard and Lloyd-Jones, Luke R. and Yengo, Loic and Yap, Chloe X. and Xue, Angli and Sidorenko, Julia and McRae, Allan F. and Powell, Joseph E. and Montgomery, Grant W. and Metspalu, Andres and Esko, Tonu and Gibson, Greg and Wray, Naomi R. and Visscher, Peter M. and Yang, Jian}, issn = {1061-4036}, journal = {Nature Genetics}, number = {5}, pages = {746--753}, publisher = {Springer Nature}, title = {{Signatures of negative selection in the genetic architecture of human complex traits}}, doi = {10.1038/s41588-018-0101-4}, volume = {50}, year = {2018}, } @inproceedings{78, abstract = {We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.}, author = {Bakhirkin, Alexey and Ferrere, Thomas and Nickovic, Dejan and Maler, Oded and Asarin, Eugene}, isbn = {978-3-030-00150-6}, location = {Bejing, China}, pages = {215 -- 232}, publisher = {Springer}, title = {{Online timed pattern matching using automata}}, doi = {10.1007/978-3-030-00151-3_13}, volume = {11022}, year = {2018}, } @article{6, abstract = {Lesion and electrode location verification are traditionally done via histological examination of stained brain slices, a time-consuming procedure that requires manual estimation. Here, we describe a simple, straightforward method for quantifying lesions and locating electrodes in the brain that is less laborious and yields more detailed results. Whole brains are stained with osmium tetroxide, embedded in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes of the brains with resolutions and virtual section thicknesses dependent on the sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively). Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays, electrolytic lesions, and silicon probes can also be localized. Free and proprietary software allows experimenters to examine the sample volume from any plane and segment the volume manually or automatically. Because this method generates whole brain volume, lesions and electrodes can be quantified to a much higher degree than in current methods, which will help standardize comparisons within and across studies.}, author = {Masís, Javier and Mankus, David and Wolff, Steffen and Guitchounts, Grigori and Jösch, Maximilian A and Cox, David}, journal = {Journal of visualized experiments}, publisher = {MyJove Corporation}, title = {{A micro-CT-based method for characterising lesions and locating electrodes in small animal brains}}, doi = {10.3791/58585}, volume = {141}, year = {2018}, }