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Reservoir computing

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https://www.readbyqxmd.com/read/29450674/risk-assessment-of-pesticides-in-estuaries-a-review-addressing-the-persistence-of-an-old-problem-in-complex-environments
#1
Nagore Cuevas, Marta Martins, Pedro M Costa
Estuaries, coastal lagoons and other transition ecosystems tend to become the ultimate reservoirs of pollutants transported by continental runoff, among which pesticides constitute the class of most concern. High amounts of dissolved and particulated organic matter greatly contribute to the accumulation of pesticides that eventually become trapped in sediments or find their way along food chains. Perhaps not so surprisingly, it is common to find elevated levels of pesticides in estuarine sediments decades after their embargo...
February 15, 2018: Ecotoxicology
https://www.readbyqxmd.com/read/29446725/mapping-of-protein-protein-interactions-web-based-resources-for-revealing-interactomes
#2
Branislava Gemovic, Neven Sumonja, Radoslav Davidovic, Vladimir Perovic, Nevena Veljkovic
BACKGROUND: The significant number of protein-protein interactions (PPIs) discovered by harnessing concomitant advances in the fields of sequencing, crystallography, spectrometry and two-hybrid screening suggests astonishing prospects for remodelling drug discovery. The PPI space which includes up to 650 000 entities is a remarkable reservoir of potential therapeutic targets for every human disease. In order to allow modern drug discovery programs to leverage this we should be able to discern complete PPI maps associated with a specific disorder and corresponding normal physiology...
February 13, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29422504/low-loss-photonic-reservoir-computing-with-multimode-photonic-integrated-circuits
#3
Andrew Katumba, Jelle Heyvaert, Bendix Schneider, Sarah Uvin, Joni Dambre, Peter Bienstman
We present a numerical study of a passive integrated photonics reservoir computing platform based on multimodal Y-junctions. We propose a novel design of this junction where the level of adiabaticity is carefully tailored to capture the radiation loss in higher-order modes, while at the same time providing additional mode mixing that increases the richness of the reservoir dynamics. With this design, we report an overall average combination efficiency of 61% compared to the standard 50% for the single-mode case...
February 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29400491/ion-transport-and-precipitation-kinetics-as-key-aspects-of-stress-generation-on-pore-walls-induced-by-salt-crystallization
#4
A Naillon, P Joseph, M Prat
The stress generation on pore walls due to the growth of a sodium chloride crystal in a confined aqueous solution is studied from evaporation experiments in microfluidic channels in conjunction with numerical computations of crystal growth. The study indicates that the stress buildup on the pore walls is a highly transient process taking place over a very short period of time (in less than 1 s in our experiments). The analysis makes clear that what matters for the stress generation is not the maximum supersaturation at the onset of the crystal growth but the supersaturation at the interface between the solution and the crystal when the latter is about to be confined between the pore walls...
January 19, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29380955/endogenous-dipeptidyl-peptidase-iv-modulates-skeletal-muscle-arteriolar-diameter-in-rats
#5
Leslie E Neidert, Mohammed Al-Tarhuni, Daniel Goldman, Heidi A Kluess, Dwayne N Jackson
The purpose of this study is to investigate that dipeptidyl peptidase IV (DPP-IV) released from skeletal and vascular smooth muscle can increase arteriolar diameter in a skeletal muscle vascular bed by reducing neuropeptide Y (NPY)-mediated vasoconstriction. We hypothesized that the effect of myokine DPP-IV would be greatest in the smallest and least in the largest arterioles. Eight male Sprague Dawley rats (age 7-9 weeks; mass, mean ± SD: 258 ± 41 g) were anesthetized and the gluteus maximus dissected in situ for intravital microscopy analysis of arteriolar diameter of the vascular network...
January 2018: Physiological Reports
https://www.readbyqxmd.com/read/29376715/model-free-prediction-of-large-spatiotemporally-chaotic-systems-from-data-a-reservoir-computing-approach
#6
Jaideep Pathak, Brian Hunt, Michelle Girvan, Zhixin Lu, Edward Ott
We demonstrate the effectiveness of using machine learning for model-free prediction of spatiotemporally chaotic systems of arbitrarily large spatial extent and attractor dimension purely from observations of the system's past evolution. We present a parallel scheme with an example implementation based on the reservoir computing paradigm and demonstrate the scalability of our scheme using the Kuramoto-Sivashinsky equation as an example of a spatiotemporally chaotic system.
January 12, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29368157/fluorescence-correlation-spectroscopy-with-photobleaching-correction-in-slowly-diffusing-systems
#7
Cameron Hodges, Rudra P Kafle, J Damon Hoff, Jens-Christian Meiners
Fluorescence correlation spectroscopy (FCS) is a powerful tool to quantitatively study the diffusion of fluorescently labeled molecules. It allows in principle important questions of macromolecular transport and supramolecular aggregation in living cells to be addressed. However, the crowded environment inside the cells slows diffusion and limits the reservoir of labeled molecules, causing artifacts that arise especially from photobleaching and limit the utility of FCS in these applications. We present a method to compute the time correlation function from weighted photon arrival times, which compensates computationally during the data analysis for the effect of photobleaching...
January 24, 2018: Journal of Fluorescence
https://www.readbyqxmd.com/read/29358410/transit-time-and-age-distributions-for-nonlinear-time-dependent-compartmental-systems
#8
Holger Metzler, Markus Müller, Carlos A Sierra
Many processes in nature are modeled using compartmental systems (reservoir/pool/box systems). Usually, they are expressed as a set of first-order differential equations describing the transfer of matter across a network of compartments. The concepts of age of matter in compartments and the time required for particles to transit the system are important diagnostics of these models with applications to a wide range of scientific questions. Until now, explicit formulas for transit-time and age distributions of nonlinear time-dependent compartmental systems were not available...
January 22, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29355604/in-depth-phylodynamics-evolutionary-analysis-and-in-silico-predictions-of-universal-epitopes-of-influenza-a-subtypes-and-influenza-b-viruses
#9
Ricardo Durães-Carvalho, Marco Salemi
This study applied High-Performance Computing to explore the high-resolution phylodynamics and the evolutionary dynamics of Influenza viruses (IVs) A and B and their subtypes in-depth to identify peptide-based candidates for broad-spectrum vaccine targets. For this purpose, we collected all the available Hemagglutinin (HA) and Neuraminidase (NA) nucleotide and amino acid sequences (more than 100,000) of IVs isolated from all the reservoirs and intermediate hosts species, from all geographic ranges and from different isolation sources, covering a period of almost one century of sampling years...
January 19, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29347020/macroscopic-violation-of-the-law-of-heat-conduction
#10
Michael M Cândido, Welles A M Morgado, Sílvio M Duarte Queirós
We analyze a model describing an anharmonic macroscopic chain in contact with general reservoirs that follow the Lévy-Itô theorem on the Gaussian-Poissonian decomposition of the measure. We do so by considering a perturbative approach to compute the heat flux and the (canonical) temperature profile when the system reaches the steady state. This approach allows observing a macroscopic violation of the law of the heat conduction equivalent to that found for small (N=2) systems in contact with general reservoirs, which conveys the ascendency of the nature of the reservoirs over the size of the system...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29332951/soil-seal-development-under-simulated-rainfall-structural-physical-and-hydrological-dynamics
#11
Elena Armenise, Robert W Simmons, Sujung Ahn, Amin Garbout, Stefan H Doerr, Sacha J Mooney, Craig J Sturrock, Karl Ritz
This study delivers new insights into rainfall-induced seal formation through a novel approach in the use of X-ray Computed Tomography (CT). Up to now seal and crust thickness have been directly quantified mainly through visual examination of sealed/crusted surfaces, and there has been no quantitative method to estimate this important property. X-ray CT images were quantitatively analysed to derive formal measures of seal and crust thickness. A factorial experiment was established in the laboratory using open-topped microcosms packed with soil...
January 2018: Journal of Hydrology
https://www.readbyqxmd.com/read/29313334/design-of-phase-changeable-and-injectable-alginate-hydrogel-for-imaging-guided-tumor-hyperthermia-and-chemotherapy
#12
Jiulong Zhao, Jialing Li, Chunping Zhu, Fei Hu, Hongyu Wu, Xiaohua Man, Zhaoshen Li, Changqing Ye, Duowu Zou, Shige Wang
The objective of the present study was to construct an alginate (AG) phase-changeable and injectable hydrogel for imaging-guided tumor hyperthermia and chemotherapy. Based on the binding between the α-L-guluronic blocks of AG and calcium ions, the AG/MoS2/Bi2S3-PEG (MBP)/doxorubicin (DOX) solution formed a cross-linked hydrogel to simultaneously encapsulate MBP nanosheets and DOX within the hydrogel matrix. The in situ-formed hydrogel can act as a reservoir to control the release of entrapped drug molecules, and the doped MBP nanosheets and DOX can realize computed tomography/photoacoustic dual-modal imaging-guided in vivo tumor PTT and chemotherapy, respectively...
January 9, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29300746/a-neural-network-model-for-the-orbitofrontal-cortex-and-task-space-acquisition-during-reinforcement-learning
#13
Zhewei Zhang, Zhenbo Cheng, Zhongqiao Lin, Chechang Nie, Tianming Yang
Reinforcement learning has been widely used in explaining animal behavior. In reinforcement learning, the agent learns the value of the states in the task, collectively constituting the task state space, and uses the knowledge to choose actions and acquire desired outcomes. It has been proposed that the orbitofrontal cortex (OFC) encodes the task state space during reinforcement learning. However, it is not well understood how the OFC acquires and stores task state information. Here, we propose a neural network model based on reservoir computing...
January 4, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29289131/from-classical-to-quantum-and-back-hamiltonian-adaptive-resolution-path-integral-ring-polymer-and-centroid-molecular-dynamics
#14
Karsten Kreis, Kurt Kremer, Raffaello Potestio, Mark E Tuckerman
Path integral-based methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, including path-integral molecular dynamics, which allows for the calculation of quantum statistical properties, and ring-polymer and centroid molecular dynamics, which allow the calculation of approximate quantum dynamical properties...
December 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29289043/using-machine-learning-to-replicate-chaotic-attractors-and-calculate-lyapunov-exponents-from-data
#15
Jaideep Pathak, Zhixin Lu, Brian R Hunt, Michelle Girvan, Edward Ott
We use recent advances in the machine learning area known as "reservoir computing" to formulate a method for model-free estimation from data of the Lyapunov exponents of a chaotic process. The technique uses a limited time series of measurements as input to a high-dimensional dynamical system called a "reservoir." After the reservoir's response to the data is recorded, linear regression is used to learn a large set of parameters, called the "output weights." The learned output weights are then used to form a modified autonomous reservoir designed to be capable of producing an arbitrarily long time series whose ergodic properties approximate those of the input signal...
December 2017: Chaos
https://www.readbyqxmd.com/read/29259188/reservoir-computing-using-dynamic-memristors-for-temporal-information-processing
#16
Chao Du, Fuxi Cai, Mohammed A Zidan, Wen Ma, Seung Hwan Lee, Wei D Lu
Reservoir computing systems utilize dynamic reservoirs having short-term memory to project features from the temporal inputs into a high-dimensional feature space. A readout function layer can then effectively analyze the projected features for tasks, such as classification and time-series analysis. The system can efficiently compute complex and temporal data with low-training cost, since only the readout function needs to be trained. Here we experimentally implement a reservoir computing system using a dynamic memristor array...
December 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/29205576/investigation-of-me4n-scf3-as-a-stable-solid-safe-reservoir-for-s-cf2-as-a-surrogate-for-thiophosgene
#17
Thomas Scattolin, Maoping Pu, Franziska Schoenebeck
While thiophosgene finds widespread usage on a multi-ton scale, its fluorinated counterpart S=CF2 is essentially unexplored in synthesis. Using experimental reactivity tests, ReactIR and computational techniques, we herein showcase that the solid (Me4N)SCF3 functions as a safe reservoir for S=CF2. A key feature is that the reactive electrophile is not simply released over time, but instead is liberated under activation with a protic nucleophile. The reactivity of S=CF2 is mild, allowing large-scale and late-stage synthetic applications without special reaction control...
December 4, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29197514/mathematical-analysis-of-the-transmission-dynamics-of-the-liver-fluke-opisthorchis-viverrini
#18
Christine Bürli, Helmut Harbrecht, Peter Odermatt, Somphou Sayasone, Nakul Chitnis
We develop and analyse two population-based models of the transmission dynamics of the worm parasite Opisthorchis viverrini. The life cycle of O. viverrini includes humans, cats and dogs as definitive hosts; and snails and fish as intermediate hosts. The first model has only one definitive host (humans) while the second model has two additional hosts: the reservoir hosts, cats and dogs. We define reproduction numbers and endemic equilibrium points for the two models. We use prevalence data for the five hosts from two islands in Lao People's Democratic Republic to estimate distributions of parameter values...
November 29, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29196846/the-availability-of-water-associated-with-glycogen-during-dehydration-a-reservoir-or-raindrop
#19
Roderick F G J King, Ben Jones, John P O'Hara
PURPOSE: This study evaluated whether glycogen-associated water is a protected entity not subject to normal osmotic homeostasis. An investigation into practical and theoretical aspects of the functionality of this water as a determinant of osmolality, dehydration, and glycogen concentration was undertaken. METHODS: In vitro experiments were conducted to determine the intrinsic osmolality of glycogen-potassium phosphate mixtures as would be found intra-cellularly at glycogen concentrations of 2% for muscle and 5 and 10% for liver...
December 1, 2017: European Journal of Applied Physiology
https://www.readbyqxmd.com/read/29186875/distribution-and-inferred-evolutionary-characteristics-of-a-chimeric-ssdna-virus-associated-with-intertidal-marine-isopods
#20
Kalia S I Bistolas, Ryan M Besemer, Lars G Rudstam, Ian Hewson
Aquatic invertebrates are common reservoirs of a rapidly expanding group of circular Rep-encoding ssDNA (CRESS-DNA) viruses. This study identified and explored the phylogenetic relationship between novel CRESS-DNA viral genotypes associated with Pacific intertidal isopods Idotea wosnesenskii, Idotea resecata, and Gnorimosphaeroma oregonensis. One genotype associated with I. wosnesenskii, IWaV278, shared sequence similarity and genomic features with Tombusviridae (ssRNA) and Circoviridae (ssDNA) genomes and was putatively assigned to the Cruciviridae clade comprising chimeric viruses...
November 26, 2017: Viruses
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