Reservoir computing

Extraintestinal pathogenic Escherichia coli (ExPEC) are important pathogens in humans and certain animals. Molecular epidemiological analyses of ExPEC are based on structured observations of E. coli strains as they occur in the wild. By assessing real-world phenomena as they occur in authentic contexts and hosts, they provide an important complement to experimental assessment. Fundamental to the success of molecular epidemiological studies are the careful selection of subjects and the use of appropriate typing methods and statistical analysis...

To accommodate structured approaches of neural computation, we propose a class of recurrent neural networks for indexing and storing sequences of symbols or analog data vectors. These networks with randomized input weights and orthogonal recurrent weights implement coding principles previously described in vector symbolic architectures (VSA) and leverage properties of reservoir computing. In general, the storage in reservoir computing is lossy, and cross-talk noise limits the retrieval accuracy and information capacity...

The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system's electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions...

Mobile phones and tablet computers may be contaminated with microorganisms and become a potential reservoir for cross-transmission of pathogens between healthcare workers and patients. There is no generally accepted guidance how to reduce contamination on mobile devices in healthcare settings. Our aim was to determine the efficacy of the Codonics D6000™ UV-C disinfection device. Daily disinfection reduced contamination on screens and on protective cases (test) significantly, but not all cases (control) could be decontaminated...

Leishmania donovani is the primary cause of a fatal disease visceral leishmaniasis (VL) in East Africa and in the Indian subcontinent. Human beings are the only known reservoir of L. donovani and due to the emergence and the spread of drug resistance control for this disease is become worse. Therefore, identification of novel drug target is very important to develop new drug and combat drug resistance issue. Experimental determination of target is costly and time-consuming, hence it is necessary to first identify the efficient target with the accurate mathematical method and then further go for in vitro/in vivo study...

Human immunodeficiency virus (HIV) enters the brain early after infecting humans and may remain in the central nervous system despite successful antiretroviral treatment. Many neuroimaging techniques were used to study HIV+ patients with or without opportunistic infections. These techniques assessed abnormalities in brain structures (using computed tomography, structural magnetic resonance imaging (MRI), diffusion MRI) and function (using functional MRI at rest or during a task, and perfusion MRI with or without a contrast agent)...

Generalized synchronization between coupled dynamical systems is a phenomenon of relevance in applications that range from secure communications to physiological modelling. Here, we test the capabilities of reservoir computing and, in particular, echo state networks for the detection of generalized synchronization. A nonlinear dynamical system consisting of two coupled Rössler chaotic attractors is used to generate temporal series consisting of time-locked generalized synchronized sequences interleaved with unsynchronized ones...

On Svalbard, Arctic Norway, an unconventional siliciclastic reservoir, relying on (micro)fractures for enhanced fluid flow in a low-permeable system, is investigated as a potential CO2 sequestration site. The fractures' properties at depth are, however, poorly understood. High resolution X-ray computed tomography (micro-CT) imaging allows one to visualize such geomaterials at reservoir conditions. We investigated reservoir samples from the De Geerdalen Formation on Svalbard to understand the influence of fracture closure on the reservoir fluid flow behavior...

In this study, we investigate the use of multifunctional smart radiotherapy biomaterials (SRBs) loaded with immunoadjuvants for boosting the abscopal effect of local radiotherapy (RT). SRBs were designed similar to currently used inert RT biomaterials, incorporating a biodegradable polymer with reservoir for loading payloads of the immunoadjuvant anti-CD40 monoclonal antibody. Lung (LLC1) tumors were generated both on the right and left flank of each mouse, with the left tumor representing metastasis. The mice were randomized and divided into eight cohorts with four cohorts receiving image-guided RT (IGRT) at 5 Gy and another similar four cohorts at 0 Gy...

Canonical molecular dynamics simulations of crystal growth from solution suffer from severe finite-size effects. As the crystal grows, the solute molecules are drawn from the solution to the crystal leading to a continuous drop in the solution concentration. This is in contrast to experiments in which the crystal grows at an approximately constant supersaturation of a bulk solution. Recently, Perego et al. [J. Chem. Phys., 142, 144113 (2015)] have shown that in a periodic set-up in which the crystal is represented as a slab, the concentration in the vicinity of the two surfaces can be kept constant while the molecules are drawn from a part of the solution that acts as a molecular reservoir...

Geologic storage of carbon dioxide (CO2 ) is considered a viable strategy for significantly reducing anthropogenic CO2 emissions into the atmosphere; however, understanding the flow mechanisms in various geological formations is essential for safe storage using this technique. This study presents, for the first time, a two-phase (CO2 and brine) flow visualization under reservoir conditions (10 MPa, 50 °C) for a highly heterogeneous conglomerate core obtained from a real CO2 storage site. Rock heterogeneity and the porosity variation characteristics were evaluated using X-ray computed tomography (CT)...

A formalism, called H-theory, is applied to the problem of statistical equilibrium of a hierarchical complex system with multiple time and length scales. In this approach, the system is formally treated as being composed of a small subsystem-representing the region where the measurements are made-in contact with a set of "nested heat reservoirs" corresponding to the hierarchical structure of the system, where the temperatures of the reservoirs are allowed to fluctuate owing to the complex interactions between degrees of freedom at different scales...

Background: Afebrile Plasmodium falciparum infections usually remain undetected and untreated in the community and could potentially contribute to sustaining local malaria transmission in areas aiming for malaria elimination. Methods: Thirty-two men with afebrile P. falciparum infections detected with rapid diagnostic test (RDTs) were followed for 28 days. Kaplan-Meier estimates were computed to estimate probability of parasite positivity and of reducing parasitaemia by half of its initial level by day 28...

We experimentally investigate delay-based photonic reservoir computing using semiconductor lasers with optical feedback and injection. We apply different types of temporal mask signals, such as digital, chaos, and colored-noise mask signals, as the weights between the input signal and the virtual nodes in the reservoir. We evaluate the performance of reservoir computing by using a time-series prediction task for the different mask signals. The chaos mask signal shows superior performance than that of the digital mask signals...

Physical, chemical and mechanical pore-scale (i.e. micrometer-scale) mechanisms in rock are of key importance in many, if not all, subsurface processes. These processes are highly relevant in various applications, e.g. hydrocarbon recovery, CO2 geo-sequestration, geophysical exploration, water production, geothermal energy production, or the prediction of the location of valuable hydrothermal deposits. Typical examples are multi-phase flow (e.g. oil and water) displacements driven by buoyancy, viscous or capillary forces, mineral-fluid interactions (e...

Volcanic lakes are characterized by physicochemical favorable conditions for the development of reservoirs of C-bearing greenhouse gases that can be dispersed to air during occasional rollover events. By combining a microbiological and geochemical approach, we showed that the chemistry of the CO2- and CH4-rich gas reservoir hosted within the meromictic Lake Averno (Campi Flegrei, southern Italy) are related to the microbial niche differentiation along the vertical water column. The simultaneous occurrence of diverse functional groups of microbes operating under different conditions suggests that these habitats harbor complex microbial consortia that impact on the production and consumption of greenhouse gases...

Few studies have utilized molecular epidemiological methods to study transmission links to clinical isolates in intensive care units. 94 multi-drug resistant organisms (MDRO) cultured from routine specimens from ICU patients over 13 weeks were stored (11 MRSA, 2 VRE and 81 Gram-negative bacteria). Medical staff personal mobile phones, departmental phones and ICU keyboards were swabbed and cultured for MDRO; MRSA was isolated from two phones. Environmental and patient isolates of the same genus were selected for whole genome sequencing...

Agriculture is one of the environmental/economic sectors that may adversely be affected by climate change, especially, in already nowadays water-scarce regions, like the Middle East. One way to cope with future changes in absolute as well as seasonal (irrigation) water amounts can be the adaptation of the agricultural crop pattern in a region, i.e. by planting crops which still provide high yields and so economic benefits to farmers under such varying climate conditions. To do this properly, the whole cascade starting from climate change, effects on hydrology and surface water availability, subsequent effects on crop yield, agricultural areas available, and, finally, economic value of a multi-crop cultivation pattern must be known...

Despite having notable advantages over established machine learning methods for time series analysis, reservoir computing methods, such as echo state networks (ESNs), have yet to be widely used for practical data mining applications. In this paper, we address this deficit with a case study that demonstrates how ESNs can be trained to predict disease labels when stimulated with movement data. Since there has been relatively little prior research into using ESNs for classification, we also consider a number of different approaches for realising input-output mappings...

Advective particle tracking is a conventional groundwater modeling technique that is widely used as a screening tool but lacks robustness as a reliable method for general applications. In this work, we investigate the suitability of industry-standard, finite-difference, grid-based methods as an alternative to the conventional particle-tracking approach. The presented method is classified as a particular case of the more general forward- or backward-in-time advective-dispersive probabilistic transport approaches...