scholarly journals Resolving challenges in quantitative modeling of microbial community dynamics

2018 ◽  
Author(s):  
Samuel F. M. Hart ◽  
Hanbing Mi ◽  
Robin Green ◽  
Li Xie ◽  
Jose Mario Bello Pineda ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Rapid Evolution ◽  
Model Performance ◽  
Experimental Results ◽  
Model Parameters ◽  
Microbial Community Dynamics ◽  
Improve Model ◽  
Measured Strain ◽  
Community Environments ◽  
Almost All

AbstractMicrobial communities can perform biochemical activities that monocultures cannot. Controlling communities requires an understanding of community dynamics. Here, we mathematically predict the growth rate of an engineered community consisting of two S. cerevisiae strains, each releasing a metabolite required and consumed by the partner. Initial model parameters were based on strain phenotypes measured in batch mono-cultures with zero or excess metabolite, and failed to quantitatively predict experimental results. To resolve model-experiment discrepancy, we chemically identified the correct exchanged metabolites, but this did not improve model performance. We then re-measured strain phenotypes in chemostats mimicking the metabolite-limited community environments, while mitigating or incorporating effects of rapid evolution. Almost all phenotypes we measured varied significantly with the metabolite environment. Once we used parameters measured in community-like chemostat environments, prediction agreed with experimental results. In summary, using a simplified community, we uncovered, and devised means to resolve, modeling challenges that are likely general.

scholarly journals Metagenomics: Retrospect and Prospects in High Throughput Age

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Satish Kumar ◽  
Kishore Kumar Krishnani ◽  
Bharat Bhushan ◽  
Manoj Pandit Brahmane
Keyword(s):  
Community Dynamics ◽  
Full Potential ◽  
Basic Study ◽  
Independent Manner ◽  
Microbial Community Dynamics ◽  
Current State ◽  
Culture Independent ◽  
Almost All ◽  
Insight Into ◽  
Generation Sequencing

In recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. In the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. A brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenomes of diverse habitats. The present review also highlights the paradigm shift of metagenomics from basic study of community composition to insight into the microbial community dynamics for harnessing the full potential of uncultured microbes with more emphasis on the implication of breakthrough developments, namely, Next Generation Sequencing, advanced bioinformatics tools, and systems biology.

Holdup and holdup profiles in the reciprocating plate extractor VPE

1990 ◽  
Vol 55 (11) ◽  
pp. 2648-2661 ◽  
Author(s):  
Helena Sovová ◽  
Vladislav Bízek ◽  
Jaroslav Procházka
Keyword(s):  
Steady State ◽  
Experimental Results ◽  
Model Parameters ◽  
Dispersed Phase ◽  
Pulse Form ◽  
Sieve Plates

In this work measurements of mean holdup of dispersed phase, of axial holdup profiles and of flooding points in a reciprocating plate contactor with both the VPE-type plates and the sieve plates were carried out. The experimental results were compared with a monodisperse model of steady-state column hydrodynamics and the model parameters were evaluated. Important differences in the behaviour of the two plate types could be identified. Comparison was also made between two reciprocating drives of different pulse form.

scholarly journals Comprehensive Wind and Wave Statistics and Extreme Values for Design and Analysis of Marine Structures in the Adriatic Sea

2021 ◽  
Vol 9 (5) ◽  
pp. 522
Author(s):  
Marko Katalinić ◽  
Joško Parunov
Keyword(s):  
Adriatic Sea ◽  
Extreme Values ◽  
Wave Climate ◽  
Offshore Structures ◽  
Model Parameters ◽  
Peak Period ◽  
Significant Wave ◽  
Wave Statistics ◽  
Wave Heights ◽  
Almost All

Wind and waves present the main causes of environmental loading on seagoing ships and offshore structures. Thus, its detailed understanding can improve the design and maintenance of these structures. Wind and wave statistical models are developed based on the WorldWaves database for the Adriatic Sea: for the entire Adriatic Sea as a whole, divided into three regions and for 39 uniformly spaced locations across the offshore Adriatic. Model parameters are fitted and presented for each case, following the conditional modelling approach, i.e., the marginal distribution of significant wave height and conditional distribution of peak period and wind speed. Extreme significant wave heights were evaluated for 20-, 50- and 100-year return periods. The presented data provide a consistent and comprehensive description of metocean (wind and wave) climate in the Adriatic Sea that can serve as input for almost all kind of analyses of ships and offshore structures.

scholarly journals Enhanced Neural Network Model for Worldwide Estimation of Weighted Mean Temperature

2021 ◽  
Vol 13 (12) ◽  
pp. 2405
Author(s):  
Fengyang Long ◽  
Chengfa Gao ◽  
Yuxiang Yan ◽  
Jinling Wang
Keyword(s):  
Neural Network ◽  
Real Time ◽  
Model Performance ◽  
Global Scale ◽  
Radiosonde Data ◽  
Model Parameters ◽  
Measured Temperature ◽  
Weighted Mean ◽  
Weighted Mean Temperature ◽  
Application Scope

Precise modeling of weighted mean temperature (Tm) is critical for realizing real-time conversion from zenith wet delay (ZWD) to precipitation water vapor (PWV) in Global Navigation Satellite System (GNSS) meteorology applications. The empirical Tm models developed by neural network techniques have been proved to have better performances on the global scale; they also have fewer model parameters and are thus easy to operate. This paper aims to further deepen the research of Tm modeling with the neural network, and expand the application scope of Tm models and provide global users with more solutions for the real-time acquisition of Tm. An enhanced neural network Tm model (ENNTm) has been developed with the radiosonde data distributed globally. Compared with other empirical models, the ENNTm has some advanced features in both model design and model performance, Firstly, the data for modeling cover the whole troposphere rather than just near the Earth’s surface; secondly, the ensemble learning was employed to weaken the impact of sample disturbance on model performance and elaborate data preprocessing, including up-sampling and down-sampling, which was adopted to achieve better model performance on the global scale; furthermore, the ENNTm was designed to meet the requirements of three different application conditions by providing three sets of model parameters, i.e., Tm estimating without measured meteorological elements, Tm estimating with only measured temperature and Tm estimating with both measured temperature and water vapor pressure. The validation work is carried out by using the radiosonde data of global distribution, and results show that the ENNTm has better performance compared with other competing models from different perspectives under the same application conditions, the proposed model expanded the application scope of Tm estimation and provided the global users with more choices in the applications of real-time GNSS-PWV retrival.

scholarly journals Towards Robust Representations of Spatial Networks Using Graph Neural Networks

2021 ◽  
Vol 11 (15) ◽  
pp. 6918
Author(s):  
Chidubem Iddianozie ◽  
Gavin McArdle
Keyword(s):  
Machine Learning ◽  
Model Performance ◽  
Network Models ◽  
Data Representation ◽  
Spatial Networks ◽  
Neural Network Models ◽  
Improve Model ◽  
Graph Neural Networks ◽  
Spatial Entities ◽  
Improve Model Performance

The effectiveness of a machine learning model is impacted by the data representation used. Consequently, it is crucial to investigate robust representations for efficient machine learning methods. In this paper, we explore the link between data representations and model performance for inference tasks on spatial networks. We argue that representations which explicitly encode the relations between spatial entities would improve model performance. Specifically, we consider homogeneous and heterogeneous representations of spatial networks. We recognise that the expressive nature of the heterogeneous representation may benefit spatial networks and could improve model performance on certain tasks. Thus, we carry out an empirical study using Graph Neural Network models for two inference tasks on spatial networks. Our results demonstrate that heterogeneous representations improves model performance for down-stream inference tasks on spatial networks.

scholarly journals Population Pharmacokinetics of Doxycycline in Children

2019 ◽  
Vol 63 (12) ◽  
Author(s):  
Elizabeth J. Thompson ◽  
Huali Wu ◽  
Chiara Melloni ◽  
Stephen Balevic ◽  
Janice E. Sullivan ◽  
...  
Keyword(s):  
Model Performance ◽  
Standard Of Care ◽  
Volume Of Distribution ◽  
Clinical Value ◽  
Final Model ◽  
Childhood Infections ◽  
Obesity Status ◽  
Improve Model ◽  
Using Data ◽  
Improve Model Performance

ABSTRACT Doxycycline is a tetracycline-class antimicrobial labeled by the U.S. Food and Drug Administration for children >8 years of age for many common childhood infections. Doxycycline is not labeled for children ≤8 years of age, due to the association between tetracycline-class antibiotics and tooth staining, although doxycycline may be used off-label under severe conditions. Accordingly, there is a paucity of pharmacokinetic (PK) data to guide dosing in children 8 years and younger. We leveraged opportunistically collected plasma samples after intravenous (i.v.) and oral doxycycline doses received per standard of care to characterize the PK of doxycycline in children of different ages and evaluated the effect of obesity and fasting status on PK parameters. We developed a population PK model of doxycycline using data collected from 47 patients 0 to 18 years of age, including 14 participants ≤8 years. We developed a 1-compartment PK model and found doxycycline clearance to be 3.32 liters/h/70 kg of body weight and volume to be 96.8 liters/70 kg for all patients, comparable to values reported in adults. We estimated a bioavailability of 89.6%, also consistent with adult data. Allometrically scaled clearance and volume of distribution did not differ between children 2 to ≤8 years of age and children >8 to ≤18 years of age, suggesting that younger children may be given the same per-kilogram dosing. Obesity status and fasting status were not selected for inclusion in the final model. Additional doxycycline PK samples collected in future studies may be used to improve model performance and maximize its clinical value.

High resolution single cell analytics to follow microbial community dynamics in anaerobic ecosystems

Methods ◽  
2012 ◽  
Vol 57 (3) ◽  
pp. 338-349 ◽  
Author(s):  
Susann Müller ◽  
Thomas Hübschmann ◽  
Sabine Kleinsteuber ◽  
Carsten Vogt
Keyword(s):  
Microbial Community ◽  
High Resolution ◽  
Single Cell ◽  
Community Dynamics ◽  
Microbial Community Dynamics ◽  
Resolution Single

scholarly journals Characterization of Moisture Diffusion in Cured Concrete Slabs at Early Ages

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Xiao Zhang ◽  
Hongduo Zhao
Keyword(s):  
Process Model ◽  
Model Simulation ◽  
Moisture Diffusion ◽  
Experimental Results ◽  
Concrete Slabs ◽  
Model Parameters ◽  
Early Age ◽  
Water Curing ◽  
Early Age Concrete

The objective of this paper is to investigate the characterization of moisture diffusion inside early-age concrete slabs subjected to curing. Time-dependent relative humidity (RH) distributions of three mixture proportions subjected to three different curing methods (i.e., air curing, water curing, and membrane-forming compounds curing) and sealed condition were measured for 28 days. A one-dimensional nonlinear moisture diffusion partial differential equation (PDE) based on Fick’s second law, which incorporates the effect of curing in the Dirichlet boundary condition using a concept of curing factor, is developed to simulate the diffusion process. Model parameters are calibrated by a genetic algorithm (GA). Experimental results show that the RH reducing rate inside concrete under air curing is greater than the rates under membrane-forming compound curing and water curing. It is shown that the effect of water-to-cement (w/c) ratio on self-desiccation is significant. Lower w/c ratio tends to result in larger RH reduction. RH reduction considering both effect of diffusion and self-desiccation in early-age concrete is not sensitive to w/c ratio, but to curing method. Comparison between model simulation and experimental results indicates that the improved model is able to reflect the effect of curing on moisture diffusion in early-age concrete slabs.

Experimental Study of Ductile Fracture for Non-Aligned Multiple Flaws in a Plate

2009 ◽  
Author(s):  
Katsumasa Miyazaki ◽  
Kunio Hasegawa ◽  
Koichi Saito ◽  
Bostjan Bezensek
Keyword(s):  
Experimental Study ◽  
Ductile Fracture ◽  
Estimation Procedure ◽  
Maximum Load ◽  
Experimental Results ◽  
Collapse Load ◽  
Plate Specimen ◽  
Fracture Tests ◽  
Almost All

The fitness-for-service code requires the characterization of non-aligned multiple flaws for the flaw evaluation, which is performed using a flaw proximity rule. Worldwide almost all codes provide own proximity rule, often with unclear technical bases of the application of proximity rule to ductile fracture. To clarify the appropriate proximity rule for non-aligned multiple flaws in fully plastic fracture, fracture tests on flat plate specimen with non-aligned multiple through wall flaws were conducted at ambient temperature. The emphasis of this study was put on the flaw alignment rule, which determines whether non-aligned flaws are treated as independent or aligned onto the same plane for the purpose of flaw evaluations. The effects of the flaw separation and flaw size on the maximum load were investigated. The experimental results were compared with the estimations of the collapse load using the alignment rules in the ASME Section XI, BS7910 and API 579-1 codes. A new estimation procedure specific to the fully plastic fracture was proposed and compared with the comparison with the experimental results.

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