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Reservoir computing

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https://www.readbyqxmd.com/read/29036481/identification-of-the-direct-regulon-of-ntca-during-early-acclimation-to-nitrogen-starvation-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#1
Joaquín Giner-Lamia, Rocío Robles-Rengel, Miguel A Hernández-Prieto, M Isabel Muro-Pastor, Francisco J Florencio, Matthias E Futschik
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29031250/communication-relaxation-limited-electronic-currents-in-extended-reservoir-simulations
#2
Daniel Gruss, Alex Smolyanitsky, Michael Zwolak
Open-system approaches are gaining traction in the simulation of charge transport in nanoscale and molecular electronic devices. In particular, "extended reservoir" simulations, where explicit reservoir degrees of freedom are present, allow for the computation of both real-time and steady-state properties but require relaxation of the extended reservoirs. The strength of this relaxation, γ, influences the conductance, giving rise to a "turnover" behavior analogous to Kramers turnover in chemical reaction rates...
October 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29020980/identification-of-76-novel-b1-metallo-%C3%AE-lactamases-through-large-scale-screening-of-genomic-and-metagenomic-data
#3
Fanny Berglund, Nachiket P Marathe, Tobias Österlund, Johan Bengtsson-Palme, Stathis Kotsakis, Carl-Fredrik Flach, D G Joakim Larsson, Erik Kristiansson
BACKGROUND: Metallo-β-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly problematic class of antibiotic resistance determinants. We hypothesized that there is a large and unexplored reservoir of unknown metallo-β-lactamases, some of which may spread to pathogens, thereby threatening public health...
October 12, 2017: Microbiome
https://www.readbyqxmd.com/read/29018390/ego-depletion-in-real-time-an-examination-of-the-sequential-task-paradigm
#4
Madeleine M Arber, Michael J Ireland, Roy Feger, Jessica Marrington, Joshua Tehan, Gerald Tehan
Current research into self-control that is based on the sequential task methodology is currently at an impasse. The sequential task methodology involves completing a task that is designed to tax self-control resources which in turn has carry-over effects on a second, unrelated task. The current impasse is in large part due to the lack of empirical research that tests explicit assumptions regarding the initial task. Five studies test one key, untested assumption underpinning strength (finite resource) models of self-regulation: Performance will decline over time on a task that depletes self-regulatory resources...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28980132/qualitative-and-quantitative-metals-liberation-assessment-for-characterization-of-various-waste-printed-circuit-boards-for-recycling
#5
Anshu Priya, Subrata Hait
Metals liberation and composition are decisive attributes in characterization of e-waste for metal recycling. Though end-of-life printed circuit board (PCB) is an integral part of e-waste as secondary resource reservoir, yet no standardized procedure exists for metals liberation and dissolution for its characterization. Thus, the paper aims at assessment of metals liberation upon comminution employing scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS) followed by comparative assessment of the existing United States Environmental Protection Agency (USEPA) digestion procedures, viz...
October 4, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28968589/quantification-of-pore-size-distribution-in-reservoir-rocks-using-mri-logging-a-case-study-of-south-pars-gas-field
#6
Jalal Neshat Ghojogh, Mohammad Esmaili, Behrooz Noruzi-Masir, Puyan Bakhshi
Pore size distribution (PSD) is an important factor for controlling fluid transport through porous media. The study of PSD can be applicable in areas such as hydrocarbon storage, contaminant transport, prediction of multiphase flow, and analysis of the formation damage by mud infiltration. Nitrogen adsorption, centrifugation method, mercury injection, and X-ray computed tomography are commonly used to measure the distribution of pores. A core sample is occasionally not available because of the unconsolidated nature of reservoirs, high cost of coring operation, and program limitations...
September 23, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28954378/an-integrated-methodology-to-forecast-the-efficiency-of-nourishment-strategies-in-eroding-deltas
#7
Rafael J Bergillos, Alejandro López-Ruiz, Daniel Principal-Gómez, Miguel Ortega-Sánchez
Many deltas across the globe are retreating, and nearby beaches are undergoing strong erosion as a result. Among soft and prompt solutions, nourishments are the most heavily used. This paper presents an integrated methodology to forecast the efficiency of nourishment strategies by means of wave climate simulations, wave propagations with downscaling techniques, computation of longshore sediment transport rates and application of the one-line model. It was applied to an eroding deltaic beach (Guadalfeo, southern Spain), where different scenarios as a function of the nourished coastline morphology, input volume and grain size were tested...
September 23, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28944810/microfluidic-step-emulsification-in-axisymmetric-geometry
#8
I Chakraborty, J Ricouvier, P Yazhgur, P Tabeling, A M Leshansky
Biphasic step-emulsification (Z. Li et al., Lab Chip, 2015, 15, 1023) is a promising microfluidic technique for high-throughput production of μm and sub-μm highly monodisperse droplets. The step-emulsifier consists of a shallow (Hele-Shaw) microchannel operating with two co-flowing immiscible liquids and an abrupt expansion (i.e., step) to a deep and wide reservoir. Under certain conditions the confined stream of the disperse phase, engulfed by the co-flowing continuous phase, breaks into small highly monodisperse droplets at the step...
September 25, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28933724/an-automatic-multi-target-independent-analysis-framework-for-non-planar-infrared-visible-registration
#9
Xinglong Sun, Tingfa Xu, Jizhou Zhang, Zishu Zhao, Yuankun Li
In this paper, we propose a novel automatic multi-target registration framework for non-planar infrared-visible videos. Previous approaches usually analyzed multiple targets together and then estimated a global homography for the whole scene, however, these cannot achieve precise multi-target registration when the scenes are non-planar. Our framework is devoted to solving the problem using feature matching and multi-target tracking. The key idea is to analyze and register each target independently. We present a fast and robust feature matching strategy, where only the features on the corresponding foreground pairs are matched...
July 26, 2017: Sensors
https://www.readbyqxmd.com/read/28923777/an-improved-method-for-permeability-estimation-of-the-bioclastic-limestone-reservoir-based-on-nmr-data
#10
Xinmin Ge, Yiren Fan, Jianyu Liu, Li Zhang, Yujiao Han, Donghui Xing
Permeability is an important parameter in formation evaluation since it controls the fluid transportation of porous rocks. However, it is challengeable to compute the permeability of bioclastic limestone reservoirs by conventional methods linking petrophysical and geophysical data, due to the complex pore distributions. A new method is presented to estimate the permeability based on laboratory and downhole nuclear magnetic resonance (NMR) measurements. We divide the pore space into four intervals by the inflection points between the pore radius and the transversal relaxation time...
October 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28923058/a-model-of-plasmodium-vivax-concealment-based-on-plasmodium-cynomolgi-infections-in-macaca-mulatta
#11
Luis L Fonseca, Chester J Joyner, Mary R Galinski, Eberhard O Voit
BACKGROUND: Plasmodium vivax can cause severe malaria. The total parasite biomass during infections is correlated with the severity of disease but not necessarily quantified accurately by microscopy. This finding has raised the question whether there could be sub-populations of parasites that are not observed in peripheral blood smears but continue to contribute to the increase in parasite numbers that drive pathogenesis. Non-human primate infection models utilizing the closely related simian malaria parasite Plasmodium cynomolgi hold the potential for quantifying the magnitude of possibly unobserved infected red blood cell (iRBC) populations and determining how the presence of this hidden reservoir correlates with disease severity...
September 18, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28905430/archaea-s-layer-nanotube-from-a-black-smoker-in-complex-with-cyclo-octasulfur-s8-rings
#12
Matthew McDougall, Olga Francisco, Candice Harder-Viddal, Roy Roshko, Markus Meier, Jörg Stetefeld
Elemental sulfur exists primarily as an S80 ring and serves as terminal electron acceptor for a variety of sulfur-fermenting bacteria. Hyperthermophilic archaea from black smoker vents are an exciting research tool to advance our knowledge of sulfur respiration under extreme conditions. Here, we use a hybrid method approach to demonstrate that the proteinaceous cavities of the S-layer nanotube of the hyperthermophilic archaeon Staphylothermus marinus act as a storage reservoir for cyclo-octasulfur S8. Fully atomistic molecular dynamics (MD) simulations were performed and the method of multiconfigurational thermodynamic integration was employed to compute the absolute free energy for transferring a ring of elemental sulfur S8 from an aqueous bath into the largest hydrophobic cavity of a fragment of archaeal tetrabrachion...
September 14, 2017: Proteins
https://www.readbyqxmd.com/read/28882172/meta-analyses-of-the-proportion-of-japanese-encephalitis-virus-infection-in-vectors-and-vertebrate-hosts
#13
Ana R S Oliveira, Lee W Cohnstaedt, Erin Strathe, Luciana Etcheverry Hernández, D Scott McVey, José Piaggio, Natalia Cernicchiaro
BACKGROUND: Japanese encephalitis (JE) is a zoonosis in Southeast Asia vectored by mosquitoes infected with the Japanese encephalitis virus (JEV). Japanese encephalitis is considered an emerging exotic infectious disease with potential for introduction in currently JEV-free countries. Pigs and ardeid birds are reservoir hosts and play a major role on the transmission dynamics of the disease. The objective of the study was to quantitatively summarize the proportion of JEV infection in vectors and vertebrate hosts from data pertaining to observational studies obtained in a systematic review of the literature on vector and host competence for JEV, using meta-analyses...
September 7, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28872827/rare-earth-polyoxometalates
#14
Colette Boskovic
Longstanding and important applications make use of the chemical and physical properties of both rare earth metals and polyoxometalates of early transition metals. The catalytic, optical, and magnetic features of rare earth metal ions are well-known, as are the reversible multielectron redox and photoredox capabilities of polyoxomolybdates and polyoxotungstates. The combination of rare earth ions and polyoxometalates in discrete molecules and coordination polymers is of interest for the unique combination of chemical and physical properties that can arise...
September 5, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28867329/patchy-parasitized-skin-governs-leishmania-donovani-transmission-to-sand-flies
#15
Shaden Kamhawi, Tiago D Serafim
Doehl et al. have combined empirical data with computer simulation to demonstrate that RAG-2 mice intravenously infected with Leishmania donovani form heterogeneous skin parasite patches that govern infectiousness to sand flies. This model provides a much-needed tool to explore the relevance of asymptomatic and symptomatic visceral leishmaniasis patients as infection reservoirs.
October 2017: Trends in Parasitology
https://www.readbyqxmd.com/read/28861060/crispr-cas-systems-features-and-the-gene-reservoir-role-of-coagulase-negative-staphylococci
#16
Ciro C Rossi, Thaysa Souza-Silva, Amanda V Araújo-Alves, Marcia Giambiagi-deMarval
The claimed role of gene reservoir of coagulase-negative staphylococci (CoNS) could be contradicted by estimates that CRISPR/Cas systems are found in the genomes of 40-50% of bacteria, as these systems interfere with plasmid uptake in staphylococci. To further correlate this role with presence of CRISPR, we analyzed, by computational methods, 122 genomes from 15 species of CoNS. Only 15% of them harbored CRISPR/Cas systems, and this proportion was much lower for S. epidermidis and S. haemolyticus, the CoNS most frequently associated with opportunistic infections in humans...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28860513/reservoir-computing-beyond-memory-nonlinearity-trade-off
#17
Masanobu Inubushi, Kazuyuki Yoshimura
Reservoir computing is a brain-inspired machine learning framework that employs a signal-driven dynamical system, in particular harnessing common-signal-induced synchronization which is a widely observed nonlinear phenomenon. Basic understanding of a working principle in reservoir computing can be expected to shed light on how information is stored and processed in nonlinear dynamical systems, potentially leading to progress in a broad range of nonlinear sciences. As a first step toward this goal, from the viewpoint of nonlinear physics and information theory, we study the memory-nonlinearity trade-off uncovered by Dambre et al...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28854273/high-resolution-imaging-of-the-mitral-valve-in-the-natural-state-with-7-tesla-mri
#18
Sam E Stephens, Serguei Liachenko, Neil B Ingels, Jonathan F Wenk, Morten O Jensen
Imaging techniques of the mitral valve have improved tremendously during the last decade, but challenges persist. The delicate changes in annulus shape and papillary muscle position throughout the cardiac cycle have significant impact on the stress distribution in the leaflets and chords, thus preservation of anatomically accurate positioning is critical. The aim of this study was to develop an in vitro method and apparatus for obtaining high-resolution 3D MRI images of porcine mitral valves in both the diastolic and systolic configurations with physiologically appropriate annular shape, papillary muscle positions and orientations, specific to the heart from which the valve was harvested...
2017: PloS One
https://www.readbyqxmd.com/read/28810075/a-b-spline-framework-for-smooth-derivative-computation-in-well-test-analysis-using-diagnostic-plots
#19
Josué Tago, Antonio Hernández-Espriú
In the oil and gas industry, well test analysis using derivative plots, has been the core technique in examining reservoir and well behavior over the last three decades. Recently, diagnostics plots have gained recognition in the field of hydrogeology; however, this tool is still underused by groundwater professionals. The foremost drawback is that the derivative function must be computed from noisy field measurements, usually based on finite-difference schemes, which complicates the analysis. We propose a B-spline framework for smooth derivative computation, referred to as Constrained Quartic B-Splines with Free Knots...
August 15, 2017: Ground Water
https://www.readbyqxmd.com/read/28804119/artificial-intelligence-dna-mimicry-and-human-health
#20
George B Stefano, Richard M Kream
The molecular evolution of genomic DNA across diverse plant and animal phyla involved dynamic registrations of sequence modifications to maintain existential homeostasis to increasingly complex patterns of environmental stressors. As an essential corollary, driver effects of positive evolutionary pressure are hypothesized to effect concerted modifications of genomic DNA sequences to meet expanded platforms of regulatory controls for successful implementation of advanced physiological requirements. It is also clearly apparent that preservation of updated registries of advantageous modifications of genomic DNA sequences requires coordinate expansion of convergent cellular proofreading/error correction mechanisms that are encoded by reciprocally modified genomic DNA...
August 14, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
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