Plant trace generation for formal plant model inference: Methods and case study

Author(s):  
Dmitry Avdyukhin ◽  
Daniil Chivilikhin ◽  
Georgiy Korneev ◽  
Vladimir Ulyantsev ◽  
Anatoly Shalyto
Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1744
Author(s):  
Stefania Pilati ◽  
Giulia Malacarne ◽  
David Navarro-Payá ◽  
Gabriele Tomè ◽  
Laura Riscica ◽  
...  

The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.


2020 ◽  
Vol 13 (2) ◽  
pp. 564
Author(s):  
Renata Cristina Mafra ◽  
Mayara Maezano Faita Pinheiro ◽  
Rejane Ennes Cicerelli ◽  
Lucas Prado Osco ◽  
Marcelo Rodrigo Alves ◽  
...  

O processo erosivo é um fenômeno que acontece devido às condições climáticas ou uso inadequado da terra. O mapeamento dos níveis de vulnerabilidade à erosão de uma área pode ocorrer usando diferentes modelos de inferência geográfica. No entanto, definir o método apropriado é ainda uma questão a ser respondida. Este trabalho apresenta uma abordagem de validação de mapa de vulnerabilidade à erosão elaborado por diferentes métodos de inferência. Como estudo de caso, adotou-se uma bacia hidrográfica e considerou-se os seguintes critérios: geomorfologia, pedologia, declividade, densidade de drenagem e cobertura da terra. Dentre os métodos testados tem-se: Combinação Linear Ponderada (CLP) e três operadores Fuzzy: soma algébrica, produto algébrico e gamma, variando o expoente “γ” entre os valores 0,4; 0,6 e 0,8. Os pesos dos critérios foram definidos com base no Processo Analítico Hierárquico. A validação dos mapas ocorreu usando 1902 pontos, sendo 951 pontos de erosão na área, definidos com base em imagens do Google Earth Pro, e 951 pontos sem erosão, gerados aleatoriamente no QGIS 3.8. O modelo de regressão logística foi usado parar comparar o desempenho de cada mapa ao apontar as áreas com maior e menor grau de vulnerabilidade. A melhor modelagem foi alcançada com o operador Fuzzy gamma quando parametrizado com γ = 0,6. Embora o CLP seja a abordagem recorrente em estudos ambientais envolvendo inferência geográfica, nossos resultados demostram que outros operadores podem produzir resultados mais próximos aos encontrados com a realidade observada em campo.  Machine learning erosion and vulnerability map validation A B S T R A C TErosion is a natural phenomenon that happens in all ecosystems, whether due to weather conditions or inappropriate land use. Mapping the erosion vulnerability levels of an area can occur using different methods of geographic inference. However, defining the appropriate method is still a question to be answered. This paper presents an erosion vulnerability map validation approach elaborated by different inference methods. As a case study, a watershed was adopted and the following criteria were considered: geomorphology, pedology, slope, drainage density and land cover. Among the tested methods are: Weighted Linear Combination (WLC) and three Fuzzy operators: algebraic sum, algebraic product and gamma, varying the exponent “γ” between the values 0.4; 0.6 and 0.8. The weights of the criteria were defined based on the Hierarchical Analytical Process. The validation of the maps took place using 1902 points, with 951 erosion points in the area defined based on Google Earth Pro images and 951 points without erosion randomly generated in QGIS 3.8. The logistic regression model was used to compare the performance of each map by pointing out the areas with the highest and lowest degree of vulnerability. The best modeling was achieved with the Fuzzy gamma operator when parameterized with γ = 0.6. Although WLC is the recurring approach in environmental studies involving geographic inference, our results show that other operators can produce results closer to those encountered with the reality observed in the field.Keywords: Geographical inference; multicriteria analysis; data validation; environmental impact.


2010 ◽  
Vol 38 (3) ◽  
pp. 531-550 ◽  
Author(s):  
Sven Buerki ◽  
Félix Forest ◽  
Nadir Alvarez ◽  
Johan A. A. Nylander ◽  
Nils Arrigo ◽  
...  

2001 ◽  
Vol 43 (7) ◽  
pp. 157-165 ◽  
Author(s):  
A. Rivas ◽  
E. Ayesa ◽  
A. Galarza ◽  
A. Salterain

This paper presents a mathematical formulation for the optimum design of a new activated sludge WWTP. The WWTP optimum design problem has been formulated as a Mathematical Programming problem, which is solved through a nonlinear optimisation method. The plant model has been based on the ASM1. The minimum volume of the biological reactors and the minimum total cost (including construction and exploitation costs) have been considered as optimisation criteria. Some practical results are also included, using as a case study the design of the second stage of the Galindo-Bilbao WWTP.


2006 ◽  
Vol 53 (1) ◽  
pp. 159-167 ◽  
Author(s):  
K.V. Gernaey ◽  
U. Jeppsson ◽  
D.J. Batstone ◽  
P. Ingildsen

Including a reactive settler model in a wastewater treatment plant model allows representation of the biological reactions taking place in the sludge blanket in the settler, something that is neglected in many simulation studies. The idea of including a reactive settler model is investigated for an ASM1 case study. Simulations with a whole plant model including the non-reactive Takács settler model are used as a reference, and are compared to simulation results considering two reactive settler models. The first is a return sludge model block removing oxygen and a user-defined fraction of nitrate, combined with a non-reactive Takács settler. The second is a fully reactive ASM1 Takács settler model. Simulations with the ASM1 reactive settler model predicted a 15.3% and 7.4% improvement of the simulated N removal performance, for constant (steady-state) and dynamic influent conditions respectively. The oxygen/nitrate return sludge model block predicts a 10% improvement of N removal performance under dynamic conditions, and might be the better modelling option for ASM1 plants: it is computationally more efficient and it will not overrate the importance of decay processes in the settler.


2008 ◽  
Vol 35 (10) ◽  
pp. 1025 ◽  
Author(s):  
Beata Zagórska-Marek ◽  
Marcin Szpak

Phyllotactic pattern results from genetic control of lateral primordia size (physiological or physical) relative to the size of organogenic lateral surface of shoot apical meristem (SAM). In order to understand the diversity of patterns and ontogenetic transitions of phyllotaxis we have developed a geometric model allowing changes of the above proportion in a computer simulation of SAM’s growth. The results of serial simulations confirmed that many phyllotactic patterns (including most esoteric ones) and ontogenetic transitions known from real plant model cases can be easily obtained in silico. Properties of virtual patterns often deviated from those of ideal mathematical lattices but closely resembled those of the natural ones. This proved the assumptions of the model, such as initiation in the first available space or ontogenetic changes in primordia size, to be quite realistic. Confrontation of simulation results with some sequences of real phyllotactic patterns (case study Verbena) questions the autonomy of SAM in its organogenic activity and suggests the involvement of unknown signal positioning primordia in a non-random manner in the first available space.


2021 ◽  
Author(s):  
Maja Popovic ◽  
Lorenzo Richiardi ◽  
Ghislaine Scelo ◽  
Francesca Fasanelli ◽  
Barbara Heude ◽  
...  

Abstract Mediation analysis aims at estimating to what extent the effect of an exposure on an outcome is explained by a set of mediators on the causal pathway between the exposure and the outcome. In this context, the total effect of the exposure on the outcome can be decomposed into the natural indirect effect, i.e. the effect explained by the mediators jointly, and the natural direct effect, i.e. the effect unexplained by the mediators. However finer decompositions are also possible in presence of independent or sequential mediators. As sequential mediation analysis is increasingly common in epidemiology, applied researchers have to interface with difficulties related to the application, implementation, and interpretation of the methods pro- posed in literature. We review four statistical methods to analyse multiple sequential mediators, all based on the counterfactual framework: the inverse odds ratio weight- ing approach, the inverse probability weighting approach, the imputation approach and the extended imputation approach. These approaches are described, compared and implemented using a case-study with the aim to investigate the role of adverse reproductive outcomes and infant respiratory infections on infant wheezing in the Ninfea birth cohort.


2001 ◽  
Vol 43 (7) ◽  
pp. 287-294 ◽  
Author(s):  
D. Rousseau ◽  
F. Verdonck ◽  
O. Moerman ◽  
R. Carrette ◽  
C. Thoeye ◽  
...  

Up to now, within the design/retrofit of wastewater treatment plants (WWTPs), deterministic models were used to evaluate different scenarios on their merits in terms of effluent compliance. This paper describes an approach in which a Monte Carlo engine is coupled to a deterministic treatment plant model, followed by risk interpretation in the form of concentration - duration - frequency (cdf) curves of norm exceedance. The combination of probabilistic modelling techniques with the currently available deterministic models allows to determine the probability of exceeding the effluent limits of a WWTP. This percentage of exceedance is accompanied by confidence intervals resulting from the inherent uncertainty of influent characteristics and model parameters. The approach is illustrated for a hypothetical case study, consisting of a denitrifying plant model inspired by the benchmark model described by Spanjers et al.


Turyzm ◽  
2016 ◽  
Vol 26 (2) ◽  
pp. 39-47
Author(s):  
Beata Gierczak-Korzeniowska

The aim of this article is to identify the importance of benchmarking as a source of innovation in the activities of tourism enterprises through the case study of LOT S.A. Polish Airlines. To expand, the objective was to identify the departments within the company which used benchmarking as a stimulus to create a new or improve an existing offer. The subject was an airline belonging to Star Alliance and 27 employees from selected departments. The study used questionnaires and. with managers of selected departments only, open standardized interviews. Statistical inference methods, including a chi-square test, were applied to analyse the data. Although the introduction of benchmarking in the company's structure allows for a quick escape route from a cycle of limitation in the company’s own culture and standard behaviour (and the acquisition of knowledge during the process gives rise to new and innovative ideas) the importance of this method in innovative activities did not result in any practical application. A lack of knowledge about benchmarking was noticeable, and an identification of this method with a simple competitive analysis resulted in failures in business activity as well as a lack of creativity in its application.


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