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Transitive inferences

Antonio M Martin-Platero, Brian Cleary, Kathryn Kauffman, Sarah P Preheim, Dennis J McGillicuddy, Eric J Alm, Martin F Polz
Because microbial plankton in the ocean comprise diverse bacteria, algae, and protists that are subject to environmental forcing on multiple spatial and temporal scales, a fundamental open question is to what extent these organisms form ecologically cohesive communities. Here we show that although all taxa undergo large, near daily fluctuations in abundance, microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp. We analyze a time series of 93 consecutive days of coastal plankton using a technique that allows inference of communities as modular units of interacting taxa by determining positive and negative correlations at different temporal frequencies...
January 18, 2018: Nature Communications
Adriano Barra, Giuseppe Genovese, Peter Sollich, Daniele Tantari
We study generalized restricted Boltzmann machines with generic priors for units and weights, interpolating between Boolean and Gaussian variables. We present a complete analysis of the replica symmetric phase diagram of these systems, which can be regarded as generalized Hopfield models. We underline the role of the retrieval phase for both inference and learning processes and we show that retrieval is robust for a large class of weight and unit priors, beyond the standard Hopfield scenario. Furthermore, we show how the paramagnetic phase boundary is directly related to the optimal size of the training set necessary for good generalization in a teacher-student scenario of unsupervised learning...
October 2017: Physical Review. E
Micaela Fedele, Cecilia Vernia
In this paper we solve the inverse problem for the Curie-Weiss model and its multispecies version when multiple thermodynamic states are present as in the low temperature phase where the phase space is clustered. The inverse problem consists of reconstructing the model parameters starting from configuration data generated according to the distribution of the model. We demonstrate that, without taking into account the presence of many states, the application of the inversion procedure produces very poor inference results...
October 2017: Physical Review. E
Jacob C Kimmel, Amy Y Chang, Andrew S Brack, Wallace F Marshall
Cell populations display heterogeneous and dynamic phenotypic states at multiple scales. Similar to molecular features commonly used to explore cell heterogeneity, cell behavior is a rich phenotypic space that may allow for identification of relevant cell states. Inference of cell state from cell behavior across a time course may enable the investigation of dynamics of transitions between heterogeneous cell states, a task difficult to perform with destructive molecular observations. Cell motility is one such easily observed cell behavior with known biomedical relevance...
January 16, 2018: PLoS Computational Biology
Jan de Vries, John M Archibald
Contents I. II. III. IV. ORCID References SUMMARY: Photosynthetic eukaryotes thrive anywhere there is sunlight and water. But while such organisms are exceptionally diverse in form and function, only one phototrophic lineage succeeded in rising above its substrate: the land plants (embryophytes). Molecular phylogenetic data show that land plants evolved from streptophyte algae most closely related to extant Zygnematophyceae, and one of the principal aims of plant evolutionary biology is to uncover the key features of such algae that enabled this important transition...
January 10, 2018: New Phytologist
Hidetoshi Inamine, Stephen P Ellner, Peter D Newell, Yuan Luo, Nicolas Buchon, Angela E Douglas
A priority in gut microbiome research is to develop methods to investigate ecological processes shaping microbial populations in the host from readily accessible data, such as fecal samples. Here, we demonstrate that these processes can be inferred from the proportion of ingested microorganisms that is egested and their egestion time distribution, by using general mathematical models that link within-host processes to statistics from fecal time series. We apply this framework to Drosophila melanogaster and its gut bacterium Acetobacter tropicalis Specifically, we investigate changes in their interactions following ingestion of a food bolus containing bacteria in a set of treatments varying the following key parameters: the density of exogenous bacteria ingested by the flies (low/high) and the association status of the host (axenic or monoassociated with A...
January 9, 2018: MBio
Luca F Valle, Matthew D Greer, Joanna H Shih, Tristan Barrett, Yan Mee Law, Andrew B Rosenkrantz, Haytham Shebel, Akhil Muthigi, Daniel Su, Maria J Merino, Bradford J Wood, Peter A Pinto, Andra V Krauze, Aradhana Kaushal, Peter L Choyke, Barış Türkbey, Deborah E Citrin
PURPOSE: Prostate multiparametric magnetic resonance imaging (mpMRI) has utility in detecting post-radiotherapy local recurrence. We conducted a multireader study to evaluate the diagnostic performance of mpMRI for local recurrence after low dose rate (LDR) brachytherapy. METHODS: A total of 19 patients with biochemical recurrence after LDR brachytherapy underwent 3T endorectal coil mpMRI with T2-weighted imaging, dynamic contrast-enhanced imaging (DCE) and diffusion-weighted imaging (DWI) with pathologic confirmation...
January 2018: Diagnostic and Interventional Radiology: Official Journal of the Turkish Society of Radiology
Nahren Manuel Mascarenhas, Vishram L Terse, Shachi Gosavi
The folded structure of the heterodimeric sweet protein monellin mimics single-chain proteins of the topology β1-α1-β2-β3-β4-β5 (chain A: β3-β4-β5 and chain B: β1-α1-β2). Further, like naturally occurring single-chain proteins of a similar size, monellin folds cooperatively with no detectable intermediates. However, the two monellin chains, A and B, are marginally structured in isolation and fold only upon binding to each other. Thus, monellin presents a unique opportunity to understand the design of intrinsically disordered proteins that fold upon binding...
January 5, 2018: Journal of Physical Chemistry. B
Chia-Hong Tsai, Sahra Uygun, Rebecca Roston, Shin-Han Shiu, Christoph Benning
Facing adverse conditions such as nitrogen (N) deprivation, microalgae enter cellular quiescence, a reversible cell cycle arrest with drastic changes in metabolism allowing cells to remain viable. Recovering from N deprivation and quiescence is an active and orderly process as we are showing here for Chlamydomonas reinhardtii. We conducted comparative transcriptomics on this alga to discern processes relevant to quiescence in the context of N deprivation and recovery following refeeding. A mutant with slow recovery from N deprivation, compromised hydrolysis of triacylglycerols 7 (cht7), was included to better define the regulatory processes governing the respective transitions...
December 29, 2017: Plant Physiology
Frederico Martins, Filip K Malinowski, Peter D Nissen, Saeed Fallahi, Geoffrey C Gardner, Michael J Manfra, Charles M Marcus, Ferdinand Kuemmeth
We use a one-electron quantum dot as a spectroscopic probe to study the spin properties of a gate-controlled multielectron GaAs quantum dot at the transition between odd and even occupation numbers. We observe that the multielectron ground-state transitions from spin-1/2-like to singletlike to tripletlike as we increase the detuning towards the next higher charge state. The sign reversal in the inferred exchange energy persists at zero magnetic field, and the exchange strength is tunable by gate voltages and in-plane magnetic fields...
December 1, 2017: Physical Review Letters
Danesh Moradigaravand, Theodore Gouliouris, Beth Blane, Plamena Naydenova, Catherine Ludden, Charles Crawley, Nicholas M Brown, M Estée Török, Julian Parkhill, Sharon J Peacock
BACKGROUND: Enterococcus faecium is a leading cause of hospital-acquired infection, particularly in the immunocompromised. Here, we use whole genome sequencing of E. faecium to study within-host evolution and the transition from gut carriage to invasive disease. METHODS: We isolated and sequenced 180 E. faecium from four immunocompromised patients who developed bloodstream infection during longitudinal surveillance of E. faecium in stool and their immediate environment...
December 27, 2017: Genome Medicine
Stacey D Smith, Ricardo Kriebel
Flower form is one of many floral features thought to be shaped by pollinator-mediated selection. Although the drivers of variation in flower shape have often been examined in microevolutionary studies, relatively few have tested the relationship between shape evolution and shifts in pollination system across clades. In the present study, we use morphometric approaches to quantify shape variation across the Andean clade Iochrominae and estimate the relationship between changes in shape and shifts in pollination system using phylogenetic comparative methods...
December 27, 2017: Evolution; International Journal of Organic Evolution
Elise Delaforge, Jaka Kragelj, Laura Tengo, Andrés Palencia, Sigrid Milles, Guillaume Bouvignies, Nicola Salvi, Martin Blackledge, Malene Ringkjøbing Jensen
Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state...
December 25, 2017: Journal of the American Chemical Society
Berend van der Meer, Emma Lathouwers, Frank Smallenburg, Laura Filion
Using computer simulations, we study the dynamics and interactions of interstitial particles in hard-sphere interstitial solid solutions. We calculate the free-energy barriers associated with their diffusion for a range of size ratios and densities. By applying classical transition state theory to these free-energy barriers, we predict the diffusion coefficients, which we find to be in good agreement with diffusion coefficients as measured using event-driven molecular dynamics simulations. These results highlight that transition state theory can capture the interstitial dynamics in the hard-sphere model system...
December 21, 2017: Journal of Chemical Physics
Loan Huynh, Chris Neale, Régis Pomès, Hue Sun Chan
Biomolecular recognition entails attractive forces for the functional native states and discrimination against potential nonnative interactions that favor alternate stable configurations. The challenge posed by the competition of nonnative stabilization against native-centric forces is conceptualized as frustration. Experiment indicates that frustration is often minimal in evolved biological systems although nonnative possibilities are intuitively abundant. Much of the physical basis of minimal frustration in protein folding thus remains to be elucidated...
December 19, 2017: PLoS Computational Biology
C J Villabona Arenas, N Vidal, S Ahuka Mundeke, J Muwonga, L Serrano, J J Muyembe, F Boillot, E Delaporte, M Peeters
Molecular epidemiological studies revealed that the epicenter of the HIV pandemic was Kinshasa, the capital city of the Democratic Republic of the Congo (DRC) in Central Africa. All known subtypes and numerous complex recombinant strains co-circulate in the DRC. Moreover, high intra-subtype diversity has been also documented. During two previous surveys on HIV-1 antiretroviral drug resistance in the DRC, we identified two divergent subtype C lineages in the protease and partial reverse transcriptase gene regions...
July 2017: Virus Evolution
Ralph S Peters, Oliver Niehuis, Simon Gunkel, Marcel Bläser, Christoph Mayer, Lars Podsiadlowski, Alexey Kozlov, Alexander Donath, Simon van Noort, Shanlin Liu, Xin Zhou, Bernhard Misof, John Heraty, Lars Krogmann
Chalcidoidea are a megadiverse group of mostly parasitoid wasps of major ecological and economical importance that are omnipresent in almost all extant terrestrial habitats. The timing and pattern of chalcidoid diversification is so far poorly understood and has left many important questions on the evolutionary history of Chalcidoidea unanswered. In this study, we infer the early divergence events within Chalcidoidea and address the question of whether or not ancestral chalcidoids were small egg-parasitoids...
December 13, 2017: Molecular Phylogenetics and Evolution
Aidin Rashidi, Christopher L Wirth
This article describes the simulated Brownian motion of a sphere comprising hemispheres of unequal zeta potential (i.e., "Janus" particle) very near a wall. The simulation tool was developed and used to assist in the methodology development for applying Total Internal Reflection Microscopy (TIRM) to anisotropic particles. Simulations of the trajectory of a Janus sphere with cap density matching that of the base particle very near a boundary were used to construct 3D potential energy landscapes that were subsequently used to infer particle and solution properties, as would be done in a TIRM measurement...
December 14, 2017: Journal of Chemical Physics
Daniel Schlauch, Kimberly Glass, Craig P Hersh, Edwin K Silverman, John Quackenbush
BACKGROUND: Specific cellular states are often associated with distinct gene expression patterns. These states are plastic, changing during development, or in the transition from health to disease. One relatively simple extension of this concept is to recognize that we can classify different cell-types by their active gene regulatory networks and that, consequently, transitions between cellular states can be modeled by changes in these underlying regulatory networks. RESULTS: Here we describe MONSTER, MOdeling Network State Transitions from Expression and Regulatory data, a regression-based method for inferring transcription factor drivers of cell state conditions at the gene regulatory network level...
December 13, 2017: BMC Systems Biology
Satoru Koda, Yoshihiko Onda, Hidetoshi Matsui, Kotaro Takahagi, Yukiko Yamaguchi-Uehara, Minami Shimizu, Komaki Inoue, Takuhiro Yoshida, Tetsuya Sakurai, Hiroshi Honda, Shinto Eguchi, Ryuei Nishii, Keiichi Mochida
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis...
2017: Frontiers in Plant Science
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