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transitive inference

Abigail J Moore, Jurriaan M de Vos, Lillian P Hancock, Eric Goolsby, Erika J Edwards
Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (∼2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis...
September 25, 2017: Systematic Biology
Matthieu Gilson, Gustavo Deco, Karl Friston, Patric Hagmann, Dante Mantini, Viviana Betti, Gian Luca Romani, Maurizio Corbetta
Our behavior entails a flexible and context-sensitive interplay between brain areas to integrate information according to goal-directed requirements. However, the neural mechanisms governing the entrainment of functionally specialized brain areas remain poorly understood. In particular, the question arises whether observed changes in the regional activity for different cognitive conditions are explained by modifications of the inputs to the brain or its connectivity? We observe that transitions of fMRI activity between areas convey information about the tasks performed by 19 subjects, watching a movie versus a black screen (rest)...
October 9, 2017: NeuroImage
Yoram Zarai, Michael Margaliot, Tamir Tuller
We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called the ribosome flow model with extended objects (RFMEO). This model encapsulates many realistic features of translation including non-homogeneous transition rates along mRNA, the fact that every ribosome covers several codons, and the fact that ribosomes cannot overtake one another. The RFMEO is a mean-field approximation of an important model from statistical mechanics called the totally asymmetric simple exclusion process with extended objects (TASEPEO)...
October 2017: Journal of the Royal Society, Interface
Ling-Hong Hung, Kaiyuan Shi, Migao Wu, William Chad Young, Adrian E Raftery, Ka Yee Yeung
Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel, and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminating redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem. We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time series yeast and human datasets...
October 1, 2017: GigaScience
Mark L Ioffe, Michael J Berry
Recent advances in experimental techniques have allowed the simultaneous recordings of populations of hundreds of neurons, fostering a debate about the nature of the collective structure of population neural activity. Much of this debate has focused on the empirical findings of a phase transition in the parameter space of maximum entropy models describing the measured neural probability distributions, interpreting this phase transition to indicate a critical tuning of the neural code. Here, we instead focus on the possibility that this is a first-order phase transition which provides evidence that the real neural population is in a 'structured', collective state...
October 11, 2017: PLoS Computational Biology
Arun J Singh, Stephen A Ramsey, Theresa M Filtz, Chrissa Kioussi
Gene regulatory networks, in which differential expression of regulator genes induce differential expression of their target genes, underlie diverse biological processes such as embryonic development, organ formation and disease pathogenesis. An archetypical systems biology approach to mapping these networks involves the combined application of (1) high-throughput sequencing-based transcriptome profiling (RNA-seq) of biopsies under diverse network perturbations and (2) network inference based on gene-gene expression correlation analysis...
October 10, 2017: Cellular and Molecular Life Sciences: CMLS
Klara Edel, Matthias Krieg, Dirk Grote, Holger F Bettinger
Formal removal of two bonding partners from boranes, BR3, yields borylenes, RB, which have been inferred as reactive intermediates in a number of reactions. Phenylborylene (R = C6H5; 1) is accessible from phenyldiazidoborane by photochemical extrusion of dinitrogen under matrix isolation conditions. Concomitantly, the nitrene PhNBN is formed via phenyl rearrangement. Here we used a combination of UV/vis, IR, and ESR spectroscopy under cryogenic matrix isolation conditions to investigate the properties and reactivity of phenylborylene...
October 10, 2017: Journal of the American Chemical Society
Xiao Zhou, Desislava Hristova, Anastasios Noulas, Cecilia Mascolo, Max Sklar
Being able to assess the impact of government-led investment onto socio-economic indicators in cities has long been an important target of urban planning. However, owing to the lack of large-scale data with a fine spatio-temporal resolution, there have been limitations in terms of how planners can track the impact and measure the effectiveness of cultural investment in small urban areas. Taking advantage of nearly 4 million transition records for 3 years in London from a popular location-based social network service, Foursquare, we study how the socio-economic impact of government cultural expenditure can be detected and predicted...
September 2017: Royal Society Open Science
P J Skrodzki, M Burger, I Jovanovic
High-peak-power fs-laser filaments offer unique characteristics attractive to remote sensing via techniques such as remote laser-induced breakdown spectroscopy (R-LIBS). The dynamics of several ablation mechanisms following the interaction between a filament and a solid determines the emission strength and reproducibility of target plasma, which is of relevance for R-LIBS applications. We investigate the space- and time-resolved dynamics of ionic and atomic emission from copper as well as the surrounding atmosphere in order to understand limitations of fs-filament-ablation for standoff energy delivery...
October 6, 2017: Scientific Reports
Nibedita Das, Satyendra Singh, Amish G Joshi, Meganathan Thirumal, V Raghavendra Reddy, Laxmi Chand Gupta, Ashok Kumar Ganguli
We synthesized double perovskite Pr2FeCrO6 by solid-state method. Analysis of its X-ray powder diffraction shows that the compound crystallizes in a centrosymmetric structure with space group Pbnm. Our X-ray photoelectron spectroscopy (XPS) studies show that all the cations are present in +3 oxidation state. Magnetization studies of Pr2FeCrO6 show that the material is paramagnetic at room temperature and undergoes a magnetic transition below TCM = 250 K. We observe clear magnetic hysteresis loop, for example, below 150 K...
October 6, 2017: Inorganic Chemistry
Melike Bildirici, Özgür Ömer Ersin
The study aims to combine the autoregressive distributed lag (ARDL) cointegration framework with smooth transition autoregressive (STAR)-type nonlinear econometric models for causal inference. Further, the proposed STAR distributed lag (STARDL) models offer new insights in terms of modeling nonlinearity in the long- and short-run relations between analyzed variables. The STARDL method allows modeling and testing nonlinearity in the short-run and long-run parameters or both in the short- and long-run relations...
October 5, 2017: Environmental Science and Pollution Research International
Zahra Shamsi, Alexander S Moffett, Diwakar Shukla
One of the major challenges in atomistic simulations of proteins is efficient sampling of pathways associated with rare conformational transitions. Recent developments in statistical methods for computation of direct evolutionary couplings between amino acids within and across polypeptide chains have allowed for inference of native residue contacts, informing accurate prediction of protein folds and multimeric structures. In this study, we assess the use of distances between evolutionarily coupled residues as natural choices for reaction coordinates which can be incorporated into Markov state model-based adaptive sampling schemes and potentially used to predict not only functional conformations but also pathways of conformational change, protein folding, and protein-protein association...
October 5, 2017: Scientific Reports
Johannes Wild, Thomas N G Meier, Simon Pöllath, Matthias Kronseder, Andreas Bauer, Alfonso Chacon, Marco Halder, Marco Schowalter, Andreas Rosenauer, Josef Zweck, Jan Müller, Achim Rosch, Christian Pfleiderer, Christian H Back
Magnetic skyrmions are topologically protected whirls that decay through singular magnetic configurations known as Bloch points. We used Lorentz transmission electron microscopy to infer the energetics associated with the topological decay of magnetic skyrmions far from equilibrium in the chiral magnet Fe1-x Co x Si. We observed that the lifetime τ of the skyrmions depends exponentially on temperature, [Formula: see text]. The prefactor τ0 of this Arrhenius law changes by more than 30 orders of magnitude for small changes of the magnetic field, reflecting a substantial reduction of the lifetime of skyrmions by entropic effects and, thus, an extreme case of enthalpy-entropy compensation...
September 2017: Science Advances
Jos R Wendrich, Barbara K Möller, Song Li, Shunsuke Saiga, Rosangela Sozzani, Philip N Benfey, Bert De Rybel, Dolf Weijers
In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem, a group of slowly dividing quiescent center cells is thought to limit stem cell activity to directly neighboring cells, thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction to the more gradual changes in cell division potential and differentiation that occur as cells move further away from the quiescent center...
October 2, 2017: Proceedings of the National Academy of Sciences of the United States of America
Jiaqi Wu, Takahiro Yonezawa, Hirohisa Kishino
Life history and behavioral traits are often difficult to discern from the fossil record, but evolutionary rates of genes and their changes over time can be inferred from extant genomic data. Under the neutral theory, molecular evolutionary rate is a product of mutation rate and the proportion of neutral mutations [1, 2]. Mutation rates may be shared across the genome, whereas proportions of neutral mutations vary among genes because functional constraints vary. By analyzing evolutionary rates of 1,185 genes in a phylogeny of 89 mammals, we extracted historical profiles of functional constraints on these rates in the form of gene-branch interactions...
October 9, 2017: Current Biology: CB
Elizabeth L Jockusch
Jointed, segmented appendages are a key innovation of arthropods. The subsequent diversification of these appendages, both along the body axis and across taxa, has contributed to the evolutionary success of arthropods. Both developmental and fossil data are informative for understanding how these transitions occurred. Comparative analyses help to pinpoint the developmental novelties that distinguish arthropod appendages from the lobopodous appendages of other panarthropods, and that distinguish different appendage types...
September 1, 2017: Integrative and Comparative Biology
David Gokhman, Anat Malul, Liran Carmel
Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more...
October 1, 2017: Molecular Biology and Evolution
Julie J Lee, Mehdi Keramati
Decision-making in the real world presents the challenge of requiring flexible yet prompt behavior, a balance that has been characterized in terms of a trade-off between a slower, prospective goal-directed model-based (MB) strategy and a fast, retrospective habitual model-free (MF) strategy. Theory predicts that flexibility to changes in both reward values and transition contingencies can determine the relative influence of the two systems in reinforcement learning, but few studies have manipulated the latter...
September 2017: PLoS Computational Biology
Anthony Piot, Jan Hackel, Pascal-Antoine Christin, Guillaume Besnard
We demonstrate that rbcL underwent strong positive selection during the C 3 -C 4 photosynthetic transitions in PACMAD grasses, in particular the 3' end of the gene. In contrast, selective pressures on other plastid genes vary widely and environmental drivers remain to be identified. Plastid genomes have been widely used to infer phylogenetic relationships among plants, but the selective pressures driving their evolution have not been systematically investigated. In our study, we analyse all protein-coding plastid genes from 113 species of PACMAD grasses (Poaceae) to evaluate the selective pressures driving their evolution...
September 27, 2017: Planta
Weiming Hu, Guodong Tian, Yongxin Kang, Chunfeng Yuan, Stephen Maybank
In this paper, a new nonparametric Bayesian model called the dual sticky hierarchical Dirichlet process hidden Markov model (HDP-HMM) is proposed for mining activities from a collection of time series data such as trajectories. All the time series data are clustered. Each cluster of time series data, corresponding to a motion pattern, is modeled by an HMM. Our model postulates a set of HMMs that share a common set of states (topics in an analogy with topic models for document processing), but have unique transition distributions...
September 25, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
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