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Transitive inferences

Denis Warshan, Anton Liaimer, Eric Pederson, Sea-Yong Kim, Nicole Shapiro, Tanja Woyke, Bjørn Altermark, Katharina Pawlowski, Philip D Weyman, Christopher L Dupont, Ulla Rasmussen
The cyanobacteria belonging to the genus Nostoc comprise free-living strains but also facultative plant-symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here we compared the genomes derived from eleven symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history...
March 15, 2018: Molecular Biology and Evolution
José R Agudo, Jiwon Han, Jinyoung Park, Sinyoung Kwon, Soebiakto Loekman, Giovanni Luzi, Christoph Linderberger, Antonio Delgado, Andreas Wierschem
Two different experimental methods for determining the threshold of particle motion as a function of geometrical properties of the bed from laminar to turbulent flow conditions are presented. For that purpose, the incipient motion of a single bead is studied on regular substrates that consist of a monolayer of fixed spheres of uniform size that are regularly arranged in triangular and quadratic symmetries. The threshold is characterized by the critical Shields number. The criterion for the onset of motion is defined as the displacement from the original equilibrium position to the neighboring one...
February 22, 2018: Journal of Visualized Experiments: JoVE
Junling Long, H S Ku, Xian Wu, Xiu Gu, Russell E Lake, Mustafa Bal, Yu-Xi Liu, David P Pappas
Quantum networks will enable extraordinary capabilities for communicating and processing quantum information. These networks require a reliable means of storage, retrieval, and manipulation of quantum states at the network nodes. A node receives one or more coherent inputs and sends a conditional output to the next cascaded node in the network through a quantum channel. Here, we demonstrate this basic functionality by using the quantum interference mechanism of electromagnetically induced transparency in a transmon qubit coupled to a superconducting resonator...
February 23, 2018: Physical Review Letters
Pascal Audet, Andrew J Schaeffer
At subduction zones, the deep seismogenic transition from a frictionally locked to steady sliding interface is thought to primarily reflect changes in rheology and fluid pressure and is generally located offshore. The development of fluid pressures within a seismic low-velocity layer (LVL) remains poorly constrained due to the scarcity of dense, continuous onshore-offshore broadband seismic arrays. We image the subducting Juan de Fuca oceanic plate in northern Cascadia using onshore-offshore teleseismic data and find that the signature of the LVL does not extend into the locked zone...
March 2018: Science Advances
Yanfeng Zhang, Longyan Tian, Dong-Hui Yan, Wei He
Marssonina leaf spot disease of poplar (MLDP), caused by the hemibiotrophic pathogen Marssonina brunnea , frequently results in damage to many poplar species. In nature, two formae speciales of M. brunnea exist that are susceptible to different poplar subgenera. Marssonina brunnea f. sp. monogermtubi infects poplar hosts from Populus sect. Aigeiros (Aig), while M. brunnea f. sp. multigermtubi always infects poplar hosts from Populus sect. Leuce Duby (Leu). Based on the fungal penetration structures, a comprehensive transcriptomic approach was used to investigate the gene expression patterns of these two poplar subgenera at three crucial infection stages...
March 12, 2018: Genes
Michael Habeck, Thach Nguyen
Biological macromolecules often undergo large conformational rearrangements during a functional cycle. To simulate these structural transitions with full atomic detail typically demands extensive computational resources. Moreover, it is unclear how to incorporate, in a principled way, additional experimental information that could guide the structural transition. This article develops a probabilistic model for conformational transitions in biomolecules. The model can be viewed as a network of anharmonic springs that break, if the experimental data support the rupture of bonds...
March 9, 2018: Proteins
Muhammad Faraz Shaikh, Zoran Salcic, Kevin I-Kai Wang, Aiguo Patrick Hu
Electrical stimulators are often prescribed to correct foot drop walking. However, commercial foot drop stimulators trigger inappropriately under certain non-gait scenarios. Past researches addressed this limitation by defining stimulation control based on automaton of a gait cycle executed by foot drop of affected limb/foot only. Since gait is a collaborative activity of both feet, this research highlights the role of normal foot for robust gait detection and stimulation triggering. A novel bipedal gait model is proposed where gait cycle is realized as an automaton based on concurrent gait sub-phases (states) from each foot...
March 10, 2018: Medical & Biological Engineering & Computing
Timotheus K T Wolterbeek, Amir Raoof
Defects along wellbore interfaces constitute potential pathways for CO2 to leak from geological storage systems. In previous experimental work, we demonstrated that CO2 -induced reaction over length-scales of several meters can lead to self-sealing of such defects. In the present work, we develop a reactive transport model that, on the one hand, enables μm-mm scale exploration of reactions along debonding defects and, on the other hand, allows simulation of the large, 6 m-long samples used in our experiments...
March 8, 2018: Environmental Science & Technology
Anne-Catherine Lehours, François Enault, Dominique Boeuf, Christian Jeanthon
In marine environments, aerobic anoxygenic phototrophic (AAP) bacterial assemblages vary in space and along environmental gradients but the factors shaping their diversity and distribution at different taxonomic levels remain poorly identified. Using sets of sequences encoding the M sub-unit of the photosynthetic apparatus from different oceanic regions, we prioritized the processes underlying AAP bacterial biogeographical patterns. The present analysis offers novel insights into the ecological distribution of marine AAP bacteria and highlights that physiological constraints play a key role in structuring AAP bacterial assemblages at a global scale...
March 7, 2018: Scientific Reports
Katarína Bod'ová, Gabriel J Mitchell, Roy Harpaz, Elad Schneidman, Gašper Tkačik
Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual...
2018: PloS One
Jakub Jadwiszczak, Colin O'Callaghan, Yangbo Zhou, Daniel S Fox, Eamonn Weitz, Darragh Keane, Conor P Cullen, Ian O'Reilly, Clive Downing, Aleksey Shmeliov, Pierce Maguire, John J Gough, Cormac McGuinness, Mauro S Ferreira, A Louise Bradley, John J Boland, Georg S Duesberg, Valeria Nicolosi, Hongzhou Zhang
Precise tunability of electronic properties of two-dimensional (2D) nanomaterials is a key goal of current research in this field of materials science. Chemical modification of layered transition metal dichalcogenides leads to the creation of heterostructures of low-dimensional variants of these materials. In particular, the effect of oxygen-containing plasma treatment on molybdenum disulfide (MoS2 ) has long been thought to be detrimental to the electrical performance of the material. We show that the mobility and conductivity of MoS2 can be precisely controlled and improved by systematic exposure to oxygen/argon plasma and characterize the material using advanced spectroscopy and microscopy...
March 2018: Science Advances
James R Lyons, Ehsan Gharib-Nezhad, Thomas R Ayres
Measurements by the Genesis mission have shown that solar wind oxygen is depleted in the rare isotopes,17 O and18 O, by approximately 80 and 100‰, respectively, relative to Earth's oceans, with inferred photospheric values of about -60‰ for both isotopes. Direct astronomical measurements of CO absorption lines in the solar photosphere have previously yielded a wide range of O isotope ratios. Here, we reanalyze the line strengths for high-temperature rovibrational transitions in photospheric CO from ATMOS FTS data, and obtain an18 O depletion of δ18 O = -50 ± 11‰ (1σ)...
March 2, 2018: Nature Communications
Rudolf von May, Edgar Lehr, Daniel L Rabosky
The loss of hearing structures and loss of advertisement calls in many terrestrial breeding frogs (Strabomantidae) living at high elevations in South America are common and intriguing phenomena. The Andean frog genus Phrynopus Peters, 1873 has undergone an evolutionary radiation in which most species lack the tympanic membrane and tympanic annulus, yet the phylogenetic relationships among species in this group remain largely unknown. Here, we present an expanded molecular phylogeny of Phrynopus that includes 24 nominal species...
2018: PeerJ
Masayuki Kano, Aitaro Kato, Ryosuke Ando, Kazushige Obara
Deep low frequency tremors are indicators of slow slip transients in the brittle-ductile transition zone along subducting plates. Investigation of comprehensive tremor activities is therefore an important issue for understanding the seismic/aseismic characteristics in transition zones. Here, we focus on the radiated energy from tremors to reveal the along-strike heterogeneity in the strength of tremor patches. Based on a tremor catalog that more accurately evaluates radiated energy, we examine the spatio-temporal activity of tremors accompanied by slow slip events (SSEs) in western Shikoku, southwestern Japan...
February 26, 2018: Scientific Reports
Maria Pliatska, Maria Kapasa, Antonis Kokkalis, Alexander Polyzos, Dimitris Thanos
Transcription-factor-induced reprogramming of somatic cells to pluripotency is mediated via profound alterations in the epigenetic landscape. The histone variant macroH2A1 (mH2A1) is a barrier to the cellular reprogramming process. We demonstrate here that mH2A1 blocks reprogramming and contributes to the preservation of cell identity by trapping cells at the very early stages of the process, namely at the mesenchymal-to-epithelial transition (MET). We provided a comprehensive analysis of the genomic sites occupied by the mH2A1 nucleosomes in human fibroblasts and Embryonic Stem Cells and how they affect the reprogramming of fibroblasts to pluripotency...
February 26, 2018: Molecular and Cellular Biology
Dirk Schulze-Makuch, Dirk Wagner, Samuel P Kounaves, Kai Mangelsdorf, Kevin G Devine, Jean-Pierre de Vera, Philippe Schmitt-Kopplin, Hans-Peter Grossart, Victor Parro, Martin Kaupenjohann, Albert Galy, Beate Schneider, Alessandro Airo, Jan Frösler, Alfonso F Davila, Felix L Arens, Luis Cáceres, Francisco Solís Cornejo, Daniel Carrizo, Lewis Dartnell, Jocelyne DiRuggiero, Markus Flury, Lars Ganzert, Mark O Gessner, Peter Grathwohl, Lisa Guan, Jacob Heinz, Matthias Hess, Frank Keppler, Deborah Maus, Christopher P McKay, Rainer U Meckenstock, Wren Montgomery, Elizabeth A Oberlin, Alexander J Probst, Johan S Sáenz, Tobias Sattler, Janosch Schirmack, Mark A Sephton, Michael Schloter, Jenny Uhl, Bernardita Valenzuela, Gisle Vestergaard, Lars Wörmer, Pedro Zamorano
Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth...
March 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
Fernando Omar Zuloaga, Diego Leonel Salariato, Amalia Scataglini
Panicum sensu stricto is a genus of grasses (Poaceae) with nearly, according to this study, 163 species distributed worldwide. This genus is included in the subtribe Panicinae together with Louisiella, the latter with 2 species. Panicum and subtribe Panicinae are characterized by including annual or perennial taxa with open and lax panicles, and spikelets with the lower glume reduced; all taxa also share a basic chromosome number of x = 9 and a Kranz leaf blade anatomy typical of the NAD-me subtype photosynthetic pathway...
2018: PloS One
Maria De Iorio, Natacha Gallot, Beatriz Valcarcel, Lucy Wedderburn
Juvenile dermatomyositis (JDM) is a rare autoimmune disease that may lead to serious complications, even to death. We develop a 2-state Markov regression model in a Bayesian framework to characterise disease progression in JDM over time and gain a better understanding of the factors influencing disease risk. The transition probabilities between disease and remission state (and vice versa) are a function of time-homogeneous and time-varying covariates. These latter types of covariates are introduced in the model through a latent health state function, which describes patient-specific health over time and accounts for variability among patients...
February 20, 2018: Statistics in Medicine
Kari A Prassack, Michael C Pante, Jackson K Njau, Ignacio de la Torre
Fossil bird data (community composition and taphonomic profiles) are used here to infer the environmental context of the Oldowan-Acheulean transitional period at Olduvai Gorge, Tanzania. This is the first comprehensive report on the Middle Bed II avifauna and includes fossils excavated by the Olduvai Geochronology and Archaeology Project (OGAP) and recently rediscovered fossils collected by Mary Leakey. Crane, ibis, darter, owl, raptor, crow, and vulture are reported from Bed II for the first time. The presence of these taxa, absent earlier in this Bed, point to a general opening and drying of the landscape with grassland and open woodland expansion...
February 16, 2018: Journal of Human Evolution
Tobias Bluhmki, Claudia Schmoor, Dennis Dobler, Markus Pauly, Juergen Finke, Martin Schumacher, Jan Beyersmann
We suggest a wild bootstrap resampling technique for nonparametric inference on transition probabilities in a general time-inhomogeneous Markov multistate model. We first approximate the limiting distribution of the Nelson-Aalen estimator by repeatedly generating standard normal wild bootstrap variates, while the data is kept fixed. Next, a transformation using a functional delta method argument is applied. The approach is conceptually easier than direct resampling for the transition probabilities. It is used to investigate a non-standard time-to-event outcome, currently being alive without immunosuppressive treatment, with data from a recent study of prophylactic treatment in allogeneic transplanted leukemia patients...
February 16, 2018: Biometrics
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