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Introduction to Cross-Entropy Clustering The R Package CEC [article]

Jacek Tabor, Przemysław Spurek, Konrad Kamieniecki, Marek Śmieja, Krzysztof Misztal
2015 arXiv   pre-print
The R Package CEC performs clustering based on the cross-entropy clustering (CEC) method, which was recently developed with the use of information theory.  ...  In this work we present a practical tutorial to CEC based on the R Package CEC. Functions are provided to encompass the whole process of clustering.  ...  The CEC package In this section the implementation of the CEC algorithm in the R Package CEC is presented. Consider first the Old Faithful data in R, see Azzalini and Bowman (1990) .  ... 
arXiv:1508.04559v1 fatcat:che74xlhprgzflaywd336mifce

Assessing Soil Key Fertility Attributes Using a Portable X-Ray Fluorescence: A Simple Method to Overcome Matrix Effect

Tiago Rodrigues Tavares, Abdul Mounem Mouazen, Elton Eduardo Novais Alves, Felipe Rodrigues dos Santos, Fábio Luiz Melquiades, Hudson Wallace Pereira de Carvalho, José Paulo Molin
2020 Agronomy  
The prediction performance observed for this solution showed comparable results to the approach based on the preprogrammed measurement package tested (Geo Exploration package, Bruker AXS, Madison, WI,  ...  Univariate regression models for the prediction of clay, cation exchange capacity (CEC), and exchangeable (ex-) K and Ca were compared with the corresponding MLR models to assess matrix effect mitigation  ...  Finally, results achieved using the Geo Exploration package data showed R 2 values comparable to the MLR and PLSR models, with R 2 values of 0.83 for CEC, 0.90 for ex-Ca, and 0.92 for clay and ex-K.  ... 
doi:10.3390/agronomy10060787 fatcat:jvilkd7hinhiriznp3z7jbwffa

An Extensible Architecture for Detecting Violations of a Cloud Environment's Constraints during Legacy Software System Migration

Soren Frey, Wilhelm Hasselbring
2011 2011 15th European Conference on Software Maintenance and Reengineering  
.> 18 <ownedRelation x s i : t y p e =" p l a t f o r m : P l a t f o r m R e l a t i o n s h i p " t o =" / / @model . 0 / @platformElement . 1 " 5181 The "Constraints" package of CEM (excerpt). 1 <e  ...  The Constraints package models the CECs and is covered in Section III-A3 in greater detail. The IaaS package and PaaS package comprise elements for the corresponding cloud service models.  ... 
doi:10.1109/csmr.2011.33 dblp:conf/csmr/FreyH11 fatcat:2icse2z3y5dfliyhmwddbjmh64

Fusing environmental variables into soil spectroscopy modeling using a novel two-step regression method

S H Adi, S Grunwald, C Tafakresnanto
2019 IOP Conference Series: Earth and Environment  
Slight model performance improvements were achieved for SOC and CEC predictions, although RPD values were within the acceptable range.  ...  However, prediction results are highly variable for soil properties without active molecular bonds within the VNIR region, such as soil pH, sum of bases (SB), and cation exchange capacity (CEC).  ...  Furthermore, soil spectra were noise-filtered using the Savitzky-Golay algorithm by utilizing the "signal" package in R [25, 26] .  ... 
doi:10.1088/1755-1315/393/1/012100 fatcat:rvyxf4qxojfyfpnrxjngvnqtaa

Direct estimation of HDL-mediated cholesterol efflux capacity from serum [article]

Sanna Kuusisto, Michael V. Holmes, Pauli Ohukainen, Antti J. Kangas, Mari Karsikas, Mika Tiainen, Markus Perola, Veikko Salomaa, Johannes Kettunen, Mika Ala-Korpela
2018 bioRxiv   pre-print
However, the estimation of HDL-CEC is based onin vitrocell assays that are laborious and hamper large-scale phenotyping.  ...  High-density lipoprotein mediated cholesterol efflux capacity (HDL-CEC) is a functional attribute that may have a protective role in atherogenesis.  ...  To evaluate model calibration, predicted and observed risk was assessed by R package rms. Hosmer-Lemeshow test was calculated by R package MKmisc.  ... 
doi:10.1101/396929 fatcat:56zbbp34jrgxvap3rjro54lzv4

Geostatistics or machine learning for mapping soil attributes and agricultural practices

Wanderson de Sousa Mendes, José Alexandre Melo Demattê, Arnaldo Sousa e Barros, Diego Fernando Urbina Salazar, Merilyn Taynara Accorsi Amorim
2020 Revista Ceres  
The methods were performed using the software R (R Development Core Team, 2019) by specific packages as it follows: OrdKrig from "automap" package (Hiemstra et al., 2009) , SVM from "e1071" package (  ...  Models RMSE r 1 IOA Random Forest Clay 73.66 0.52 0.59 CEC 1.33 0.69 0.34 V% 9.57 0.83 0.68 Cubist Clay 82.15 0.39 0.55 CEC 1.31 0.64 0.37 V% 8.56 0.86 0.72 Support  ...  Another advantage, it is to map large areas ( Figure 5 ) with close performance to geostatistical approaches (r = 0.7).  ... 
doi:10.1590/0034-737x202067040010 fatcat:ftpzatq2urh7nnvozwxlnoaxku

Characterizing The Spatial Variability Of Soil Properties And Crop Yield Using High-Resolution Remote Sensing Image And Ground-Based Data

S Khanal, J Fulton, A Klopfenstein, N Douridas, S Shearer
2017 Zenodo  
A varImp function in package "caret" in the R software (Kuhn 2017) was used for this purpose.  ...  For stepwise regression, "stepAIC" function in the "MASS" package of the R software (Kuhn and Johnson 2013) was used.  ... 
doi:10.5281/zenodo.895476 fatcat:4fz3mvv4i5b2rf7rc4flnvrlbq

Oxidized HDL, Adipokines, and Endothelial Dysfunction: A Potential Biomarker Profile for Cardiovascular Risk in Women with Obesity

Stephen J. Peterson, Joseph I. Shapiro, Ellen Thompson, Shailendra Singh, Lu Liu, Jeremy A. Weingarten, Kathleen O'Hanlon, Angelica Bialczak, Siddharth R. Bhesania, Nader G. Abraham
2018 Obesity  
Elevated CEC levels have been described in both humans and mice with obesity and diabetes. Ox-HDL has been shown to be a potent driver of adipogenesis in vivo and in vitro.  ...  The relationship among BMI, IL-6, TNFα, adiponectin, and oxidized high-density lipoprotein (Ox-HDL) with circulating endothelial cells (CECs) and endothelial progenitor cells (EPCs) has not been well studied  ...  Network analysis of these correlations was performed using the R package gplots. Graphical presentation of boxplots with superimposed scatterplots was performed using the R package ggplot2.  ... 
doi:10.1002/oby.22354 pmid:30569635 pmcid:PMC6309990 fatcat:m33et7dhivb35b2xi3ykjjtmme

A Critical Evaluation of the Relationship Between the Effective Cation Exchange Capacity and Soil Organic Carbon Content in Swiss Forest Soils

Emily F. Solly, Valentino Weber, Stephan Zimmermann, Lorenz Walthert, Frank Hagedorn, Michael W. I. Schmidt
2020 Frontiers in Forests and Global Change  
At pH > 5.5, between 59 and 83% of subsoil CEC eff. originates from exchangeable calcium, whereas in acidic soils exchangeable aluminum contributes between 21 and 44% of the CEC eff.  ...  Exchangeable iron contributes to less than 1% of the variability in CEC eff.  ...  Maps were built using R packages ("sp," "lattice," "RColorBrewer," "proj4, rworldmap," "raster," "rgdal").  ... 
doi:10.3389/ffgc.2020.00098 fatcat:6nggdr74nzbe7jcwparvzc547e

Soil Electrical Conductivity Imaging Of The Soil Profile And Its Relationship To Soil Properties

A El-Naggar, C Hedley, D Horne, P Roudier, B Clothier
2017 Zenodo  
and 0.58 for DUALEM-1s for Θv and CEC, respectively).  ...  As expected, Θv, CEC and the estimated ECa follow similar trends down the soil profile. This soil ECa imaging method shows good potential for predicting 2D depth profiles of certain soil properties.  ...  Thin plate spline regression (fields package) (Nychka et al., 2015) was used in R version 3.3.2 and RStudio 1.0.136 (R Core Team., 2016) for generating the cation exchange capacity image or model.  ... 
doi:10.5281/zenodo.891094 fatcat:syayztr6onbvbejoc7rxjsyduy

An annotation database for chemicals of emerging concern in exposome research

Jeroen Meijer, Marja Lamoree, Timo Hamers, Jean-Philippe Antignac, Sébastien Hutinet, Laurent Debrauwer, Adrian Covaci, Carolin Huber, Martin Krauss, Douglas I. Walker, Emma L. Schymanski, Roel Vermeulen (+1 others)
2021 Environment International  
Establishing a database focused on the annotation of CECs in human samples will provide new insight into the distribution and extent of exposures to a wide range of CECs in humans.  ...  In total, 145,284 entries were aggregated from various CECs data sources.  ...  The "doBy" package (Højsgaard and Halekoh, 2006) in R was used to summarize the CECs list based on unique "MS-ready" InChIKeys and duplicates were removed.  ... 
doi:10.1016/j.envint.2021.106511 pmid:33773387 fatcat:m3r3o55qn5eynowxv2zos44uru

Comparison of Artificial Neural Network and Regression Pedotransfer Function for prediction of soil cation exchange capacity at Iraq, Ray AL Jazeera, Mosul region: مقارنة بين نموذجي الشبكات العصبية والانحدار الخطي المتعدد في تخمين السعة التبادلية الكاتيونية للتربة باستخدام الدوال التحويلية في العراق في منطقة ري الجزيرة في مدينة الموصل

Sahar I. Mahmood Alobyde, Firas Shawkat Hamid, Ibrahim K. Sa
2020 Mağallaẗ al-ʿulūm al-handasiyyaẗ wa-al-tiknūlūğiyā al-maʿlūmāt  
CEC represents the number of negative charges in soil, since direct method for measuring CEC are cumbersome and time consuming Lead to the grow of indirect technique in guessing of soil CEC property.  ...  The MSE and R2 resultant by ANN model for CEC were 2.2 and 0.96 individually while these result for Multiple Regression model were 3.74 and 0.88 individually.  ...  Step_wise Multiple Linear Regression, SPSS package Ver: 25, and Artificial Neural Net Works (ANN), Mat lab package Ver: 19b Multiple linear regression model: The all-purpose aim of multiple linear regression  ... 
doi:10.26389/ajsrp.p161219 fatcat:k45kpozu4bdppmbohsk54hiyhq

A Whole Blood Molecular Signature for Acute Myocardial Infarction [article]

Evan D Muse, Eric R Kramer, Haiying Wang, Paddy Barrett, Fereshteh Parviz, Mark A Novotny, Roger S Lasken, Timothy A Jatkoe, Glenn Oliveira, Hongfan Peng, Jerry Lu, Marc C Connelly (+4 others)
2016 bioRxiv   pre-print
Thus, we aimed to identify a transcriptomic signature of AMI present in whole blood, but derived from CECs.  ...  Transcriptional patterns present in circulating endothelial cells (CEC) may provide a window into the plaque rupture process and identify a proximal biomarker for AMI.  ...  Quality controls were conducted with the affy and affyQCReport R packages.  ... 
doi:10.1101/045013 fatcat:fo5qgx6aybetnk7gh7wad3qjda

A Whole Blood Molecular Signature for Acute Myocardial Infarction

Evan D. Muse, Eric R. Kramer, Haiying Wang, Paddy Barrett, Fereshteh Parviz, Mark A. Novotny, Roger S. Lasken, Timothy A. Jatkoe, Glenn Oliveira, Hongfan Peng, Jerry Lu, Mark C. Connelly (+4 others)
2017 Scientific Reports  
Thus, we aimed to identify a transcriptomic signature of AMI present in whole blood, but derived from CECs.  ...  Transcriptional patterns present in circulating endothelial cells (CEC) may provide a window into the plaque rupture process and identify a proximal biomarker for AMI.  ...  Quality controls were conducted with the affy and affyQCReport R packages.  ... 
doi:10.1038/s41598-017-12166-0 pmid:28947747 pmcid:PMC5612952 fatcat:yoq4x34ow5c5hmywabclvjy3vy

Agriculture increases the bioavailability of silicon, a beneficial element for crop, in temperate soils

M. Caubet, S. Cornu, N. P. A. Saby, J.-D. Meunier
2020 Scientific Reports  
The latter was based on the boruta package in R 59 .  ...  Si CaCl2 was also positively correlated with CEC (r = 0.59), exchangeable Ca (r = 0.54), and CEC of < 2 µm fraction (r = 0.44).  ... 
doi:10.1038/s41598-020-77059-1 pmid:33203877 fatcat:aq6amop5rzbmveefxt5k2vavam
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