scholarly journals An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

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


Author(s):  
Dmitry Avdyukhin ◽  
Daniil Chivilikhin ◽  
Georgiy Korneev ◽  
Vladimir Ulyantsev ◽  
Anatoly Shalyto

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.


2020 ◽  
Vol 83 (11) ◽  
pp. 3239-3249
Author(s):  
Helena Mannochio-Russo ◽  
Paula Carolina P. Bueno ◽  
Anelize Bauermeister ◽  
Rafael Felipe de Almeida ◽  
Pieter C. Dorrestein ◽  
...  

Author(s):  
Ashay Saxena ◽  
Shankar Venkatagiri ◽  
Rajendra K Bandi

Increasingly, agile approaches are being followed in a distributed setup to develop software. An agile approach is characterised by the need to regularly welcome change requests and update the software artefact accordingly whereas distributed teams prefer to work towards following a plan to fulfil project objectives defined upfront. This results in contradictory tensions when agile is practised with teams operating in a globally distributed format. This chapter focuses on exploring the central conflict and discuss approaches to manage the conflicting forces in an agile distributed development setup. Furthermore, it presents an industry case study to provide more clarity on conflict management in such settings.


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